Diagnosis and Treatment of Drug Resistant Leukemia

ABSTRACT

The present invention encompasses methods and compositions useful in the diagnosis and treatment of drug resistant leukemia. The invention provides a number of genes that are differentially expressed between drug resistant and drug sensitive acute lymphoblastic leukemia (ALL). These genes act as biomarkers for drug resistant leukemia, and further serve as molecular targets for drugs useful in treating drug resistant leukemia. Accordingly, the invention provides methods of diagnosing drug resistant leukemia and methods of selecting a therapy for subjects affected by drug-resistant leukemia. The invention also provides methods for screening for compounds for treating drug-resistant leukemia, and improved methods for treating drug-resistant leukemia. Compositions of the invention include arrays, computer readable media, and kits for use in the methods of the invention.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made in part with U.S. Government support under National Institutes of Health grant nos. R37 CA36401, R01 CA78224, RO1 CA51001, RO1 CA71907, U01 GM61393, U01 GM61394, and Cancer Center Support Grant CA21765. The U.S. Government may have certain rights in this invention.

FIELD OF THE INVENTION

The present invention relates generally to genes associated with resistance to drugs used to treat leukemia and methods for using these genes to improve treatment of leukemia.

BACKGROUND OF THE INVENTION

The treatment of pediatric acute lymphoblastic leukemia has improved remarkably over the past four decades, resulting in long-term disease-free survival of approximately 80 percent (Pui and Evans (1998) N. Engl. J. Med. 339:605-615 and Pui et al. (2001) Lancet Oncol. 2:597-607. Despite this progress, the number of patients with acute lymphoblastic leukemia who are not cured with contemporary therapy exceeds the total number of children with newly diagnosed acute myeloid leukemia and most other childhood cancers. Patients whose leukemia cells exhibit in vitro resistance to antileukemic agents have a significantly worse prognosis than patients whose acute lymphoblastic leukemia cells are drug sensitive (den Boer et al. (2003) J. Clin. Oncol. 21:3262-68; Kaspers et al. (1997) Blood 90:2723-29; et al. Pieters R. (1991) Lancet 338:399-403).

Little is known about the genomic determinants of leukemia cell resistance to chemotherapy. Such knowledge would provide important new insights for overcoming drug resistance in acute lymphoblastic leukemia. Accordingly, there remains a need for the identification of genes whose expression is associated with drug resistance in leukemia.

SUMMARY OF THE INVENTION

The present invention encompasses methods and compositions useful in the diagnosis and treatment of drug resistant leukemia. The invention provides a number of genes that are differentially expressed between drug resistant and drug sensitive acute lymphoblastic leukemia (ALL). These genes act as biomarkers for drug resistant leukemia, and further serve as molecular targets for drugs useful in treating drug resistant leukemia.

Accordingly, in one embodiment the invention provides a method of diagnosing drug resistant leukemia in a subject affected by leukemia. The method comprises the steps of providing a subject expression profile of a sample from a subject affected by leukemia, providing a reference expression profile associated with resistance to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, and determining whether the subject expression profile shares sufficient similarity to the reference expression profile, where the subject is diagnosed with drug resistant leukemia if the subject expression profile shares sufficient statistical similarity to the reference expression profile.

The subject expression profile and the reference expression profile comprise values representing the expression levels of genes that are differentially expressed in drug-resistant versus drug-sensitive leukemia. In particular embodiments, the profiles comprise values representing the expression levels of genes selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B.

Tables 6A, 6B, 6C, 6D, 10A, and 10B provide genes that are differentially expressed in prednisolone-resistant ALL. Tables 7A, 7B, 7C, 7D, 11A, and 11B provide genes that are differentially expressed in vincristine-resistant ALL. Tables 8A, 8B, 8C, 8D, 12A, and 12B provide genes that are differentially expressed in L-asparaginase-resistant ALL. Tables 9A, 9B, 9C, 9D, 13A, and 13B provide genes that are differentially expressed in daunorubicin-resistant ALL. The invention also provides a method of determining the prognosis for a patient with leukemia or predicting whether a subject affected by leukemia has an increased risk of relapse. The method comprises the steps of providing a subject expression profile of a sample from the subject affected by leukemia, providing a reference expression profile associated with resistance to an antileukemic agent, and determining whether the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent. The subject affected by leukemia is predicted to have an increased risk of relapse if the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent.

In another embodiment, the invention provides a method of selecting a therapy for a subject affected by leukemia. The method comprises the steps of providing a subject expression profile of a sample from the subject affected by leukemia, providing a reference expression profile associated with resistance to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, and determining whether the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent; where the therapy selected for the subject does not comprise the antileukemic agent if the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent.

In a further aspect, the invention provides a method for screening a library of compounds to identify a compound to improve treatment of drug resistant leukemia. The method comprises the steps of providing a reference expression profile comprising one or more values representing the expression level of a gene selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B, providing a cell that is resistant to an antileukemic agent; contacting the cell with one or more compounds from the library of compounds; creating a test expression profile by determining a value representing the expression level in the cell of one or more of the genes whose expression level is represented in the reference expression profile, and determining whether the test expression profile is distinguishable the reference expression profile. If the test expression profile is distinguishable from the reference expression profile, the compound is identified as a compound useful for improving treatment of drug resistant leukemia.

In another embodiment, the invention provides a method for improving treatment of drug resistant leukemia. In one embodiment, the method comprises administering to a subject affected by drug resistant leukemia a therapy comprising an antileukemic agent and an agent that enhances the expression or activity of at least one gene selected from the genes shown in Tables 6A, 6C, 7A, 7C, 8A, 8C, 9A, 9C, 10A, 11A, 12A, and 13A. Tables 6A, 6C, and 10A provide genes whose expression is down-regulated in prednisolone-resistant ALL. Tables 7A, 7C, and 11A provide genes whose expression is down-regulated in vincristine-resistant ALL. Tables 8A, 8C, and 12A provide genes whose expression is down-regulated in L-asparaginase-resistant ALL. Tables 9A, 9C, and 13A provide genes whose expression is down-regulated in daunorubicin-resistant ALL.

In another embodiment, the method for improving treatment of drug resistant leukemia comprises administering to a subject affected by drug resistant leukemia a therapy comprising an antileukemic agent and an agent that inhibits the expression or activity of one or more genes selected from the genes shown in Tables 6B, 6D, 7B, 7D, 8B, 8D, 9B, 9D, 10B, 11B, 12B, and 13B. Tables 6B, 6D, and 10B provide genes whose expression is up-regulated in prednisolone-resistant ALL. Tables 7B, 7D, and 11B provide genes whose expression is up-regulated in vincristine-resistant ALL. Tables 8B, 8D, and 12B provide genes whose expression is up-regulated in L-asparaginase-resistant ALL. Tables 9B, 9D, and 13B provide genes whose expression is up-regulated in daunorubicin-resistant ALL.

The invention also provides an array for use in a method of diagnosing drug resistant leukemia. The array comprises a substrate having a plurality of addresses, where each address has a capture probe that can specifically bind to a nucleic acid molecule selected from the group consisting of genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B.

The invention also provides a computer-readable medium comprising digitally-encoded expression profiles having values representing the expression of a gene selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B.

In another embodiment, the invention provides a kit for diagnosing drug-resistant leukemia. The kit comprises (1) an array having a substrate with of addresses, where each address has a capture probe that can specifically bind a nucleic acid molecule selected from the group consisting of genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B; and (2) a computer-readable medium comprising digitally-encoded expression profiles having values representing the expression of a gene selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B.

DESCRIPTION OF THE FIGURE

FIG. 1 shows a Kaplan-Meier analysis of treatment outcome among patients with gene expression patterns associated with cellular resistance or sensitivity to the four antileukemic agents. Panel (a) shows disease-free survival of patients treated on the Dutch and COALL protocols. Patients are sub-grouped based on combined drug resistance gene expression scores of 172 gene probe sets for antileukemic agents (prednisolone, vincristine, L-asparaginase and daunorubicin). The 33 percent with the lowest score (Sensitive), 33 percent with an intermediate (Intermediate) and 33 percent with the highest score (Resistant) are shown. Panel B shows disease-free survival of patients treated on St. Jude Children's Research Hospital protocols. Patients were assigned to the Sensitive, Intermediate and Resistant categories using the combined drug resistance gene expression score (172 gene probe sets for four drugs) according to the same values used to assign the Dutch and COALL patients to one of these categories (panel a).

DETAILED DESCRIPTION OF THE INVENTION

The present inventions now will be described more fully hereinafter with reference to the accompanying drawings, in which some, but not all embodiments of the invention are shown. Indeed, these inventions may be embodied in many different forms and should not be construed as limited to the embodiments set forth herein; rather, these embodiments are provided so that this disclosure will satisfy applicable legal requirements.

Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the invention. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.

In the present invention, genes that are differentially expressed between drug resistant and drug sensitive leukemia are identified. These genes may be used as biomarkers for diagnosing drug resistant leukemia, and for selecting a therapy for a patient having drug resistant leukemia. The differentially expressed genes are also useful in a screening method to identify compounds that increase sensitivity to antileukemic drugs. In addition, the identified genes may serve as molecular targets for drugs useful in treating drug resistant leukemia. Accordingly, the present invention encompasses methods and compositions useful in the diagnosis and treatment of drug resistant leukemia.

Diagnostic Methods:

In one embodiment, the present invention provides a method of diagnosing drug resistant leukemia in a subject affected by leukemia. The subject affected by leukemia may be either a pediatric leukemia patient or an adult pediatric patient. By “leukemia,” it is intended a malignant proliferation of the leukopoietic tissues. In some embodiments, the leukemia is acute lymphoblastic leukemia (ALL) or acute myeloblastic leukemia (AML). In particular embodiments, the leukemia is ALL.

By “drug resistant leukemia,” it is intended leukemia in which the leukemia cells are resistant to being killed by the concentrations of antileukemic agents that are used to kill leukemia cells in drug-sensitive leukemia. In particular embodiments, the drug or drugs for which resistance is to be determined is selected from prednisolone, vincristine, L-asparaginase, and daunorubicin. The relative resistance of a leukemia cell to a drug may be determined by calculating the drug concentration that is lethal to 50% of the leukemia cells (LC-50). For the purposes of the present invention, a leukemia cell is “resistant” to a drug if the LC-50 value is equal to or greater than the value shown in the chart below:

LC-50 values for classifying leukemia cells as drug-resistant Drug LC-50 Prednisolone ≧150 μg/ml Vincristine ≧1.758 μg/ml L-asparaginase ≧0.912 IU/ml Daunorubicin ≧0.114 μg/ml

The diagnostic method comprises the steps of providing a subject expression profile of a sample from a subject affected by leukemia, providing a reference expression profile associated with resistance to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, and determining whether the subject expression profile shares sufficient similarity to the reference expression profile, where the subject affected by leukemia is diagnosed with drug resistant leukemia if the subject expression profile shares sufficient similarity to the reference expression profile.

The subject expression profile and the reference expression profile comprise values representing the expression levels of genes that are differentially expressed in drug-resistant versus drug-sensitive leukemia. In particular embodiments, the profiles comprise values representing the expression levels of genes selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B.

Tables 6A, 6B, 6C, 6D, 10A, and 10B provide genes whose expression is differentially regulated in prednisolone-resistant ALL. Accordingly, in some embodiments, the antileukemic agent is prednisolone and the subject expression profile and reference expression profile contain genes selected from the genes shown in Table 6A, 6B, 6C, 6D, 10A, and 10B.

Tables 7A, 7B, 7C, 7D, 11A, and 11B provide genes whose expression is differentially regulated in vincristine-resistant ALL. Accordingly, in some embodiments, the antileukemic agent is vincristine and the subject expression profile and reference expression profile contain genes selected from the genes shown in Table 7A, 7B, 7C, 7D, 11A, and 11B.

Tables 8A, 8B, 8C, 8D, 12A, and 12B provide genes whose expression is differentially regulated in L-asparaginase-resistant ALL. Thus, in some embodiments, the antileukemic agent is L-asparaginase and the subject expression profile and reference expression profile contain genes selected from the genes shown in Table 8A, 8B, 8C, 8D, 12A, and 12B.

Tables 9A, 9B, 9C, 9D, 13A, and 13B provide genes whose expression is differentially regulated in daunorubicin-resistant ALL. In some embodiments, the antileukemic agent is daunorubicin and the subject expression profile and reference expression profile contain genes selected from the genes shown in 9A, 9B, 9C, 9D, 13A, and 13B.

In another embodiment, the invention provides a method of selecting a therapy for a subject affected by leukemia. The method comprises the steps of providing a subject expression profile of a sample from the subject affected by leukemia, providing a reference expression profile associated with resistance to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, and determining whether the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent, where the therapy selected for the subject does not comprise the antileukemic agent if the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent.

In a related embodiment, the method of selecting a therapy for a subject affected by leukemia comprises the steps of providing a subject expression profile of a sample from the subject affected by leukemia, providing a reference expression profile associated with resistance to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, and determining whether the subject expression profile is distinguishable from the reference expression profile associated with resistance to the antileukemic agent. If the subject expression profile shares statistically significant similarity with the reference profile, then the antileukemic agent is not selected for therapy for the subject.

In these methods, the subject expression profile and the reference expression profile comprise one or more values representing the expression level of a gene having differential expression in subjects affected by drug-resistant leukemia. In particular embodiments, the profiles comprise values representing the expression levels of genes selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, OA, 10B, 11A, 11B, 12A, 12B, 13A, and 13B.

A description of methods of making and comparing expression profiles is provided elsewhere herein.

Methods of Screening for Compounds to Improve the Treatment of Drug-Resistant Leukemia

In a further aspect, the invention provides a method for screening a library of test compounds to identify a candidate compound to improve treatment of drug resistant leukemia. In one embodiment, the method comprises the steps of providing a reference expression profile associate with drug resistance, where the reference expression profile comprises one or more values representing the expression level of a gene that is differentially expressed in drug resistant leukemia, providing a cell that is resistant to an antileukemic agent; contacting the cell with one or more compounds from the library of compounds; creating a test expression profile by determining a value representing the expression level in the cell of one or more of the genes whose expression level is represented in the reference expression profile and determining whether the test expression profile is statistically distinguishable the reference expression profile. If the test expression profile is statistically distinguishable from the reference expression profile, then the compound is identified as a compound useful for improving treatment of drug resistant leukemia.

In another embodiment, the method comprises the steps of providing a reference expression profile associated with drug sensitivity, where the reference profile comprises one or more values representing the expression level of a gene that is differentially expressed in drug resistant leukemia, providing a cell that is resistant to an antileukemic agent; contacting the cell with one or more compounds from the library of compounds; creating a test expression profile by determining a value representing the expression level in the cell of one or more of the genes whose expression level is represented in the reference expression profile and determining whether the test expression profile shares statistically significant similarity to the reference expression profile. If the test expression profile shares statistically significant similarity with the reference expression profile, then the compound is identified as a compound useful for improving treatment of drug resistant leukemia.

In some embodiments, the test expression profile and the reference expression profile comprise values representing the expression of genes selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B. The genes whose expression level is measured to generate the profile will be selected based on the resistance profile of the cell. For example, if the cell is resistant to prednisolone, genes from Tables 6A, 6B, 6C, 6D, 10A, and 10B can be used. Similarly, if the cell is resistant to vincristine, genes from Tables 7A, 7B, 7C, 7D, 11A, and 11B can be used. If the cell is resistant to L-asparaginase, genes from Tables 8A, 8B, 8C, 8D, 12A, and 12B can be used. If the cell is resistant to daunorubicin, genes from Tables 9A, 9B, 9C, 9D, 13A, and 13B can be used.

The cell that is resistant to an antileukemic agent can be derived from a variety of sources including, but not limited to, single cells, a collection of cells, tissue, cell culture, bone marrow, blood, or other bodily fluids. The tissue or cell source may include a tissue biopsy sample, a cell sorted population, cell culture, or a single cell. Sources for the sample of the present invention include cells from peripheral blood or bone marrow, such as blast cells from peripheral blood or bone marrow.

In some embodiments, an expression profile is produced for the drug-resistant cell before and after it is contacted with the antileukemic agent. In this embodiment, the expression profile produced from the cell prior to contact with the test compound is the reference profile associated with drug resistance used in the method. The test expression profile generated after the contact with the compound is then compared to this reference expression profile. If the test compound alters the expression of genes associated with drug resistance such that the post-contact test expression profile is statistically distinguishable from the pre-contact reference expression profile, then the compound is identified as a candidate compound for the treatment of drug resistant leukemia. In other embodiments, the reference expression profile is an expression profile that has a statistically significant correlation with drug resistance or with drug sensitivity, but is not produced directly from the drug resistant cell.

A description of expression profiles and test compounds that may be screened according to the invention is provided elsewhere herein.

Methods of Improving Treatment of Drug-Resistant Leukemia

In one aspect, the invention provides a method for improving treatment of drug resistant leukemia. This method is based on the identification of specific genes that are either significantly up-regulated or significantly down-regulated in cells that are resistant to particular antileukemic agents. Changes in the expression of these genes are associated with drug resistant in leukemia cells. Accordingly, drug resistance in leukemia cells can be modulated by enhancing the expression or activity of down-regulated genes, or by inhibiting the expression or activity of up-regulated genes.

Accordingly, in one embodiment, the method comprises administering to a subject affected by drug resistant leukemia a therapy comprising an antileukemic agent and a second agent that enhances the expression or activity of at least one gene that is down-regulated in drug resistant leukemia. The gene that is down-regulated in drug resistant leukemia is selected from the genes shown in Tables 6A, 6C, 7A, 7C, 8A, 8C, 9A, 9C, 10A, 11A, 12A, and 13A.

Tables 6A, 6C, and 10A provide genes whose expression is down-regulated in prednisolone-resistant ALL. Accordingly, these genes and their expression products are targets for up-regulation in treating resistance to prednisolone.

Tables 7A, 7C, and 11A provide genes whose expression is down-regulated in vincristine-resistant ALL. Accordingly, these genes and their expression products are targets for up-regulation in treating resistance to vincristine.

Tables 8A, 8C, and 12A provide genes whose expression is down-regulated in L-asparaginase-resistant ALL. Accordingly, these genes and their expression products are targets for up-regulation in treating resistance to L-asparaginase.

Tables 9A, 9C, and 13A provide genes whose expression is down-regulated in daunorubicin-resistant ALL. Accordingly, these genes and their expression products are targets for up-regulation in treating resistance to daunorubicin.

In another embodiment of the method for improving treatment of drug resistant leukemia comprises administering to a subject affected by drug resistant leukemia a therapy comprising an antileukemic agent and an agent that inhibits the expression or activity of at least one gene selected from the genes shown in Tables 6B, 6D, 7B, 7D, 8B, 8D, 9B, 9D, 10B, 11B, 12B, and 13B.

Tables 6B, 6D, and 10B provide genes whose expression is up-regulated in prednisolone-resistant ALL. Accordingly, these genes and their expression products are targets for inhibition in treating resistance to prednisolone.

Tables 7B, 7D, and 11B provide genes whose expression is up-regulated in vincristine-resistant ALL. Accordingly, these genes and their expression products are targets for inhibition in treating resistance to vincristine.

Tables 8B, 8D, and 12B provide genes whose expression is up-regulated in L-asparaginase-resistant ALL. Accordingly, these genes and their expression products are targets for inhibition in treating resistance to L-asparaginase.

Tables 9B, 9D, and 13B provide genes whose expression is up-regulated in daunorubicin-resistant ALL. Accordingly, these genes and their expression products are targets for inhibition in treating resistance to daunorubicin.

Expression Profiles

As used herein, an “expression profile” comprises one or more values corresponding to a measurement of the relative abundance of a gene expression product. Such values may include measurements of RNA levels or protein abundance. Thus, the expression profile can comprise values representing the measurement of the transcriptional state or the translational state of the gene. See, U.S. Pat. Nos. 6,040,138, 5,800,992, 6,020135, 6,344,316, and 6,033,860, which are hereby incorporated by reference in their entireties.

The transcriptional state of a sample includes the identities and relative abundance of the RNA species, especially mRNAs present in the sample. Preferably, a substantial fraction of all constituent RNA species in the sample are measured, but at least a sufficient fraction to characterize the transcriptional state of the sample is measured. The transcriptional state can be conveniently determined by measuring transcript abundance by any of several existing gene expression technologies.

Translational state includes the identities and relative abundance of the constituent protein species in the sample. As is known to those of skill in the art, the transcriptional state and translational state are related.

In some embodiments, the expression profiles of the present invention are generated from samples from subjects affected by leukemia or drug-resistant leukemia, including subjects having leukemia or drug-resistant leukemia, subjects suspected of having leukemia, subjects having a propensity to develop leukemia or drug-resistant leukemia, or subjects who have previously had leukemia or drug-resistant leukemia, or subjects undergoing therapy for leukemia or drug-resistant leukemia. The samples from the subject used to generate the expression profiles of the present invention can be derived from a variety of sources including, but not limited to, single cells, a collection of cells, tissue, cell culture, bone marrow, blood, or other bodily fluids. The tissue or cell source may include a tissue biopsy sample, a cell sorted population, cell culture, or a single cell. Sources for the sample of the present invention include cells from peripheral blood or bone marrow, such as blast cells from peripheral blood or bone marrow.

In selecting a sample, the percentage of the sample that constitutes cells having differential gene expression in drug resistant versus drug sensitive leukemia should be considered. Samples may comprise at least 20%, at least 30%, at least 40%, at least 50%, at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% cells having differential expression in drug resistant versus drug sensitive leukemia, with a preference for samples having a higher percentage of such cells. In some embodiments, these cells are blast cells, such as leukemic cells. The percentage of a sample that constitutes blast cells may be determined by methods well known in the art.

In some embodiments of the present invention, the expression profiles comprise values representing the expression levels of genes that are differentially expressed in drug resistant leukemia. The term “differentially expressed” as used herein means that the measurement of a cellular constituent varies in two or more samples. The cellular constituent may be up-regulated in a sample from a subject having one physiologic condition in comparison with a sample from a subject having a different physiologic condition, or down-regulated in a sample from a subject having one physiologic condition in comparison with a sample from a subject having a different physiologic condition. The differentially expressed genes of the present invention are expressed at different levels in drug resistant leukemia and drug sensitive leukemia. Some of the differentially expressed genes are up-regulated in lymphoblasts from subjects having drug-resistant leukemia in comparison with the expression level of the same gene in drug-sensitive leukemia, while other genes are down-regulated in lymphoblasts from subjects having drug resistant leukemia in comparison with the same gene in subjects having drug sensitive leukemia. These differentially expressed genes were identified based on gene expression levels for 14,550 probes in 173 leukemia samples.

The invention provides genes that are differentially expressed in lymphoblasts that are resistant to one or more of four different antileukemic agents, prednisolone, vincristine, L-asparaginase, and daunorubicin. Tables 6A, 6B, 6C, 6D, 10A, and 10B provide genes whose expression is differentially regulated in prednisolone-resistant ALL. Tables 6A, 6C, and 10A provide genes whose expression is down-regulated in prednisolone-resistant ALL in comparison with prednisolone-sensitive ALL, while Tables 6B, 6D, and 10B provide genes whose expression is up-regulated in prednisolone-resistant ALL in comparison with prednisolone-sensitive ALL. Tables 7A, 7B, 7C, 7D, 11A, and 11B provide genes whose expression is differentially regulated in vincristine resistant ALL. Tables 7A, 7C, and 11A provide genes whose expression is down-regulated in vincristine-resistant ALL in comparison with vincristine-sensitive ALL, while Tables 7B, 7D, and 11B provide genes whose expression is up-regulated in vincristine-resistant ALL in comparison with vincristine-sensitive ALL. Tables 8A, 8B, 8C, 8D, 12A, and 12B provide genes whose expression is differentially regulated in L-asparaginase resistant ALL. Tables 8A, 8C, and 12A provide genes whose expression is down-regulated in L-asparaginase-resistant ALL in comparison with L-asparaginase-sensitive ALL, while Tables 8B, 8D, and 12B provide genes whose expression is up-regulated in L-asparaginase-resistant ALL in comparison with L-asparaginase-sensitive ALL. Tables 9A, 9B, 9C, 9D, 13A, and 13B provide genes whose expression is differentially regulated in daunorubicin resistant ALL. Tables 9A, 9C, and 13A provide genes whose expression is down-regulated in daunorubicin-resistant ALL in comparison with daunorubicin-sensitive ALL, while Tables 9B, 9D, and 13B provide genes whose expression is up-regulated in daunorubicin-resistant ALL in comparison with daunorubicin-sensitive ALL.

The expression profiles according to the invention comprise one or more values representing the expression level of a gene having differential expression in drug resistant ALL. Each expression profile contains a sufficient number of values such that the profile can be used to distinguish drug resistant leukemia from drug sensitive leukemia. In some embodiments, the expression profiles comprise only one value. In other embodiments, the expression profile comprises more than one value corresponding to a differentially expressed gene, for example at least 2 values, at least 3 values, at least 4 values, at least 5 values, at least 6 values, at least 7 values, at least 8 values, at least 9 values, at least 10 values, at least 11 values, at least 12 values, at least 13 values, at least 14 values, at least 15 values, at least 16 values, at least 17 values, at least 18 values, at least 19 values, at least 20 values, at least 22 values, at least 25 values, at least 27 values, at least 30 values, at least 35 values, at least 40 values, at least 45 values, at least 50 values, at least 75 values, at least 100 values, at least 125 values, at least 150 values, at least 175 values, at least 200 values, at least 250 values, at least 300 values, at least 400 values, at least 500 values, at least 600 values, at least 700 values, at least 800 values, at least 900 values, at least 1000 values, at least 1200 values, at least 1500 values, or at least 2000 or more values.

It is recognized that the diagnostic accuracy of diagnosing drug resistant leukemia or predicting a prognosis for a leukemia patient will vary based on the number of values contained in the expression profile. Generally, the number of values contained in the expression profile is selected such that the diagnostic accuracy is at least at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 87%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%, as calculated using methods described elsewhere herein, with an obvious preference for higher percentages of diagnostic accuracy.

It is recognized that the accuracy of diagnosing drug-resistant leukemia or determining the prognosis for a patient will vary based on the strength of the correlation between the expression levels of the differentially expressed genes and the associated physiologic condition. When the values in the expression profiles represent the expression levels of genes whose expression is strongly correlated with the physiologic condition, it may be possible to use fewer number of values in the expression profile and still obtain an acceptable level of diagnostic or prognostic accuracy.

The strength of the correlation between the expression level of a differentially expressed gene and the presence or absence of a particular physiologic state may be determined by a statistical test of significance. Methods for determining the strength of a correlation between the expression level of a differentially-expressed gene and a particular physiologic state by assigning a statistical score to the correlation are reviewed in Holloway et al. (2002) Nature Genetics Suppl. 32:481-89, Churchill (2002) Nature Genetics Suppl. 32:490-95, Quackenbush (2002) Nature Genetics Suppl. 32: 496-501; Slonim (2002) Nature Genetics Suppl. 32:502-08; and Chuaqui et al. (2002) Nature Genetics Suppl. 32:509-514; each of which is herein incorporated by reference in its entirety. The statistical scores may be used to select the genes whose expression levels have the greatest correlation with a particular physiologic state in order to increase the diagnostic or prognostic accuracy of the methods of the invention, or in order to reduce the number of values contained in the expression profile while maintaining the diagnostic or prognostic accuracy of the expression profile. By a gene whose expression level is “correlated with” a particular physiologic state, it is intended a gene whose expression shows a statistically significant correlation with the physiologic state. Such methods may be used to select the genes whose expression levels have the greatest correlation with a particular treatment outcome in order to increase the predictive accuracy of the methods of the invention.

The values in the expression profiles of the invention are measurements representing the absolute or the relative expression level of differentially expressed genes. The expression levels of these genes may be determined by any method known in the art for assessing the expression level of an RNA or protein molecule in a sample. For example, expression levels of RNA may be monitored using a membrane blot (such as used in hybridization analysis such as Northern, Southern, dot, and the like), or microwells, sample tubes, gels, beads or fibers (or any solid support comprising bound nucleic acids). See U.S. Pat. Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which are expressly incorporated herein by reference. The gene expression monitoring system may also comprise nucleic acid probes in solution. Expression levels of RNA may also be monitored using the reverse transcriptase polymerase chain reaction (e.g., TaqMan®).

In one embodiment of the invention, microarrays are used to measure the values to be included in the expression profiles. Microarrays are particularly well suited for this purpose because of the reproducibility between different experiments. DNA microarrays provide one method for the simultaneous measurement of the expression levels of large numbers of genes. Each array consists of a reproducible pattern of capture probes attached to a solid support. Labeled RNA or DNA is hybridized to complementary probes on the array and then detected by laser scanning. Hybridization intensities for each probe on the array are determined and converted to a quantitative value representing relative gene expression levels. See, the Experimental section. See also, U.S. Pat. Nos. 6,040,138, 5,800,992 and 6,020,135, 6,033,860, and 6,344,316, which are incorporated herein by reference. High-density oligonucleotide arrays are particularly useful for determining the gene expression profile for a large number of RNA's in a sample.

In one approach, total mRNA isolated from the sample is converted to labeled cRNA and then hybridized to an oligonucleotide array. Each sample is hybridized to a separate array. Relative transcript levels are calculated by reference to appropriate controls present on the array and in the sample.

In another embodiment, the values in the expression profile are obtained by measuring the abundance of the protein products of the differentially-expressed genes. The abundance of these protein products can be determined, for example, using antibodies specific for the protein products of the differentially-expressed genes. The term “antibody” as used herein refers to an immunoglobulin molecule or immunologically active portion thereof, i.e., an antigen-binding portion. Examples of immunologically active portions of immunoglobulin molecules include F(ab) and F(ab′)₂ fragments, which can be generated by treating the antibody with an enzyme such as pepsin.

The antibody can be a polyclonal, monoclonal, recombinant, e.g., a chimeric or humanized, fully human, non-human, e.g., murine, or single chain antibody. In a preferred embodiment it has effector function and can fix complement. The antibody can be coupled to a toxin or imaging agent.

A full-length protein product from a differentially-expressed gene, or an antigenic peptide fragment of the protein product can be used as an immunogen. Preferred epitopes encompassed by the antigenic peptide are regions of the protein product of the differentially expressed gene that are located on the surface of the protein, e.g., hydrophilic regions, as well as regions with high antigenicity. The antibody can be used to detect the protein product of the differentially expressed gene in order to evaluate the abundance and pattern of expression of the protein. These antibodies can also be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given therapy. Detection can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance (i.e., antibody labeling). Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include ¹²⁵I, ¹³¹I, ³⁵S or ³H.

Once the values comprised in the subject expression profile and the reference expression profile or expression profiles are established, the subject profile is compared to the reference profile to determine whether the subject expression profile is sufficiently similar to the reference profile. Alternatively, the subject expression profile is compared to a plurality of reference expression profiles to select the reference expression profile that is most similar to the subject expression profile.

Any method known in the art for comparing two or more data sets to detect similarity between them may be used to compare the subject expression profile to the reference expression profiles. To determine whether two or more expression profiles show statistically significant similarity, statistical tests may be performed to determine whether any differences between the expression profile are likely to have been achieved by a random event. Methods for comparing gene expression profiles to determine whether they share statistically significant similarity are known in the art and also reviewed in Holloway et al. (2002) Nature Genetics Suppl. 32:481-89, Churchill (2002) Nature Genetics Suppl. 32:490-95, Quackenbush (2002) Nature Genetics Suppl. 32: 496-501; Slonim (2002) Nature Genetics Suppl. 32:502-08; and Chuaqui et al. (2002) Nature Genetics Suppl. 32:509-514; each of which is herein incorporated by reference in its entirety. An expression profile is “distinguishable” or “statistically distinguishable” from a reference profile according to the invention if the two expression profiles do not share statistically significant similarity.

The accuracy of diagnosing a subject with drug resistant leukemia or predicting a prognosis for a leukemia patient by comparing an expression profile for the subject with reference expression profile associated with drug resistant depends in part on the degree of similarity between the two profiles. Therefore, are required, the stringency with which the similarity between the subject expression profile and the reference profile is evaluated should be increased. For example, in various embodiments, the p-value obtained when comparing the subject expression profile to a reference profile that shares sufficient similarity with the subject expression profile is less than 0.20, less than 0.15, less than 0.10, less than 0.09, less than 0.08, less than 0.07, less than 0.06, less than 0.05, less than 0.04, less than 0.03, less than 0.02, or less than 0.01.

In some embodiments, the expression profiles of the invention are used to select a therapy for a leukemia patient. A therapy, as used herein, refers to a course of treatment intended to reduce or eliminate the affects or symptoms of a disease, in this case leukemia. A therapy regimen will typically comprise, but is not limited to, a prescribed dosage of one or more drugs or hematopoietic stem cell transplantation. Therapies, ideally, will be beneficial and reduce the disease state but in many instances the effect of a therapy will have non-desirable effects as well. Thus, the methods of the invention are useful for monitoring the effectiveness of a therapy even when non-desirable side-effects are observed.

Arrays, Computer-Readable Medium, and Kits

The present invention provides compositions that are useful in diagnosing drug resistant leukemia and in screening for drugs to treat drug-resistant leukemia. These compositions include arrays comprising a substrate having a capture probes that can bind specifically to nucleic acid molecules that are differentially expressed in drug resistant leukemia. In another aspect, the invention also provides a computer-readable medium having digitally encoded reference profiles useful in the methods of the claimed invention. The invention also encompasses kits comprising an array of the invention and a computer-readable medium having digitally-encoded reference profiles with values representing the expression of nucleic acid molecules detected by the arrays.

The arrays of the invention comprise capture probes for detecting the differentially expressed genes of the invention. By “array” is intended a solid support or substrate with peptide or nucleic acid probes attached to the support or substrate. Arrays typically comprise a plurality of different nucleic acid or peptide capture probes that are coupled to a surface of a substrate in different, known locations. These arrays, also described as “microarrays” or colloquially “chips” have been generally described in the art, for example, in U.S. Pat. Nos. 5,143,854, 5,445,934, 5,744,305, 5,677,195, 6,040,193, 5,424,186, 6,329,143, and 6,309,831 and Fodor et al. (1991) Science 251:767-77, each of which is incorporated by reference in its entirety. These arrays may generally be produced using mechanical synthesis methods or light directed synthesis methods, which incorporate a combination of photolithographic methods and solid phase synthesis methods.

Techniques for the synthesis of these arrays using mechanical synthesis methods are described in, e.g., U.S. Pat. No. 5,384,261, incorporated herein by reference in its entirety for all purposes. Although a planar array surface is preferred, the array may be fabricated on a surface of virtually any shape or even a multiplicity of surfaces. Arrays may be peptides or nucleic acids on beads, gels, polymeric surfaces, fibers such as fiber optics, glass or any other appropriate substrate, see U.S. Pat. Nos. 5,770,358, 5,789,162, 5,708,153, 6,040,193 and 5,800,992, each of which is hereby incorporated in its entirety for all purposes. Arrays may be packaged in such a manner as to allow for diagnostics or other manipulation of an all-inclusive device. See, for example, U.S. Pat. Nos. 5,856,174 and 5,922,591 herein incorporated by reference.

The arrays provided by the present invention comprise capture probes that can specifically bind a nucleic acid molecule that is differentially expressed in leukemia risk groups, a nucleic acid molecule that is differentially expressed in drug resistant leukemia. The capture probes are designed to hybridize to target nucleic acid molecules corresponding to messenger RNAs of differentially expressed genes (such as cDNA copies of differentially expressed messenger RNAs) and allow their detection. Method of designing a probe that will hybridize with a target nucleic acid molecule are well know in the art. Any capture probe that detects a differentially expressed gene of the invention may be used in an array.

The arrays may also comprise capture probes that bind to control nucleic acid molecules. The control nucleic acid molecules can be used to normalize expression data obtained from the arrays, allowing experiments performed at different times using different arrays to be compared.

The arrays can be used to measure the expression levels of nucleic acid molecules to thereby create an expression profile for use in methods of determining the diagnosis and prognosis for leukemia patients, and in screening for compounds to improve treatment of drug-resistant leukemia.

In some embodiments, each capture probe in the array detects a nucleic acid molecule selected from the nucleic acid molecules designated in 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B 12A, 12B, 13A, and 13B. The designated nucleic acid molecules include those differentially expressed in prednisolone-resistant ALL (Tables 6A, 6B, 6C, 6D, 10A, and 10B); vincristine-resistant ALL (Tables 7A, 7B, 7C, 7D, 11A, and 11B), L-asparaginase-resistant ALL (Tables 8A, 8B, 8C, 8D, 12A, and 12B), and daunorubicin-resistant ALL (Tables 9A, 9B, 9C, 9D, 13A, and 13B).

The arrays of the invention comprise a substrate having a plurality of addresses, where each addresses has a capture probe that can specifically bind a target nucleic acid molecule. The number of addresses on the substrate varies with the purpose for which the array is intended. The arrays may be low-density arrays or high-density arrays and may contain 4 or more, 8 or more, 12 or more, 16 or more, 20 or more, 24 or more, 32 or more, 48 or more, 64 or more, 72 or more 80 or more, 96, or more addresses, or 192 or more, 288 or more, 384 or more, 768 or more, 1536 or more, 3072 or more, 6144 or more, 9216 or more, 12288 or more, 15360 or more, or 18432 or more addresses. In some embodiments, the substrate has no more than 12, 24, 48, 96, or 192, or 384 addresses, no more than 500, 600, 700, 800, or 900 addresses, or no more than 1000, 1200, 1600, 2400, or 3600 addressees.

The invention also provides a computer-readable medium comprising one or more digitally-encoded expression profiles, where each profile has one or more values representing the expression of a gene that is differentially expressed in a drug resistant leukemia. Thus, in one embodiment, the invention encompasses a computer-readable medium comprising digitally-encoded expression profiles having values representing the expression of a gene selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B. In some embodiments, the digitally-encoded expression profiles are comprised in a database. See, for example, U.S. Pat. No. 6,308,170.

The present invention also provides kits useful for diagnosing drug resistant leukemia, and for screening for drugs for treating drug resistant leukemia. These kits comprise an array and a computer readable medium. The array comprises a substrate having addresses, where the addresses have capture probes that can specifically bind nucleic acid molecules that are differentially expressed in drug resistant leukemia. The computer-readable medium has digitally-encoded expression profiles containing values representing the expression level of a nucleic acid molecule detected by the array. In some embodiments, the expression profile is a reference expression profile associated with drug-resistant leukemia. The array can be used to produce a test expression profile from a sample, and this test expression profile can then be compared to the reference profile or profiles contained in the computer readable medium to determine whether it the test profile shares similarity with the reference profile.

Thus, in one embodiment, the kit comprises (1) an array having a substrate with of addresses, where each address has a capture probe that can specifically bind a nucleic acid molecule selected from the group consisting of genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B; and (2) a computer-readable medium comprising digitally-encoded expression profiles having values representing the expression of a gene selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B.

The kits of the invention may also include methods for use in a method of diagnosing drug resistant leukemia, a method of predicting the prognosis for a leukemia patient, or a method for screening for compounds for use in improving treatment of drug leukemia. These methods are described elsewhere herein.

Methods of Screening and Therapeutic Targets

The methods and compositions of the invention may be used to screen test compounds to identify therapeutic compounds useful for the treatment of drug-resistant leukemia. In one embodiment, the test compounds are screened in a sample comprising drug-resistant primary cells representing drug resistant leukemia. After exposure to the test compound, the expression levels in the sample of one or more of the differentially-expressed genes of the invention are measured using methods described elsewhere herein. Values representing the expression levels of the differentially-expressed genes are used to generate a test expression profile. This test expression profile is then compared to a reference expression profile associated with drug-resistant leukemia to determine the similarity between the subject expression profile and the reference expression profile. If the test expression profile is distinguishable from the drug resistant reference expression profile, and shares similarity with an expression profile from a drug-sensitive sample, the test compound is identified as a candidate compound useful for the treatment of drug-resistant leukemia.

The test compounds of the present invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the ‘one-bead one-compound’ library method; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to polypeptide libraries, while the other four approaches are applicable to polypeptide, non-peptide oligomer or small molecule libraries of compounds (Lam (1997) Anticancer Drug Des. 12:145).

Examples of methods for the synthesis of molecular libraries can be found in the art, for example in DeWitt et al. (1993) Proc. Natl. Acad. Sci. USA 90:6909; Erb et al. (1994) Proc. Natl. Acad. Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al. (1993) Science 261:1303; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061; and in Gallop et al. (1994) J. Med. Chem. 37:1233. Libraries of compounds may be presented in solution (e.g., Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (U.S. Pat. No. 5,223,409), spores (U.S. Pat. No. 5,223,409), plasmids (Cull et al. (1992) Proc. Natl. Acad. Sci. USA 89:1865-1869) or on phage (Scott and Smith (1990) Science 249:386-390); (Devlin (1990) Science 249:404-406); (Cwirla et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 97:6378-6382); (Felici (1991) J. Mol. Biol. 222:301-310).

Candidate compounds include, for example, 1) peptides such as soluble peptides, including Ig-tailed fusion peptides and members of random peptide libraries (see, e.g., Lam et al. (1991) Nature 354:82-84; Houghten et al. (1991) Nature 354:84-86) and combinatorial chemistry-derived molecular libraries made of D- and/or L-configuration amino acids; 2) phosphopeptides (e.g., members of random and partially degenerate, directed phosphopeptide libraries, see, e.g., Songyang et al. (1993) Cell 72:767-778); 3) antibodies (e.g., polyclonal, monoclonal, humanized, anti-idiotypic, chimeric, and single chain antibodies as well as Fab, F(ab′)₂, Fab expression library fragments, and epitope-binding fragments of antibodies); 4) small organic and inorganic molecules (e.g., molecules obtained from combinatorial and natural product libraries; 5) zinc analogs; 6) leukotriene A₄ and derivatives; 7) classical aminopeptidase inhibitors and derivatives of such inhibitors, such as bestatin and arphamenine A and B and derivatives; 8) and artificial peptide substrates and other substrates, such as those disclosed herein above and derivatives thereof.

The present invention discloses a number of genes that are differentially expressed in drug resistant leukemia. These differentially-expressed genes are shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B. Because the expression of these genes is associated with drug resistant leukemia, these genes may play a role in resistance to antileukemic agents. Accordingly, these genes and their gene products are potential therapeutic targets that are useful in methods of screening test compounds to identify therapeutic compounds for the treatment of leukemia.

The differentially expressed genes and their expression products identified as targets in accordance with the invention may be used in conventional biochemical assays or in cell-based screening assays. Johnston, P. A. and Johnston, P. A., “Cellular Platforms for HTS: three case studies”, Drug Discovery Today 7 (6): 353-363 (March 2002); Drews, J., “Drug discovery: a historical perspective”, Science 287: 1960-1965 (2000); Valler, M. J. and Green, D., “Diversity screening versus focused screening in drug discovery”, Drug Discovery Today 5 (7): 286-293 (2000); Grepin, C. and Pernelle, C., “High-throughput screening”, Drug Discovery Today 5 (5): 212-214 (2000); “Recent patents in high-throughput screening”, Nat. Biotechnol. 18 (7): 797 (2000); White, R. E., “High-throughput screening in drug metabolism and pharmacokinetic support of drug discovery”, Ann. Rev. Pharmacol. Toxicol. 40: 133-157 (2000); Broach, J. R. and Thomer, J., “High-throughput screening for drug discovery”, Nature 384 (Suppl): 14-16 (1996); Silverman, L. et al., “New assay technologies for high-throughput screening”, Curr. Opin. Chem. Biol. 2:397-403 (1998). Such biochemical assays are based on the activity of the expression product and include standard kinase assays, phosphatase assays, binding assays, assays for apoptosis, hydroxylation, oxidation, conjugation and other enzyme reactions, and assays for protein-protein or protein-DNA or RNA interactions. Cell-based screening assays utilize recombinant host cells expressing the differentially expressed gene product. The recombinant host cells are screened to identify compounds that can activate the product of the differentially expressed gene or increase expression of the gene (i.e. agonists), or inactivate the product of the differentially expressed gene or decrease expression of the gene (i.e. antagonists).

Any of the drug resistance modifying functions mediated by the product of the differentially expressed gene may be used as an endpoint in the screening assay for identifying therapeutic compounds for the treatment of leukemia. See for example, Evans and Guy (2004) Nat. Genet. 236:214-5. Such endpoint assays include assays for cell proliferation, assays for modulation of the cell cycle, assays for the expression of markers indicative of leukemia, and assays for the expression level of genes differentially expressed in leukemia risk groups as described above.

Modulators of the activity of a product of a differentially-expressed gene identified according to these drug screening assays provided above can be used to treat a subject with drug resistant leukemia. These methods of treatment include the steps of administering the modulators of the activity of a product of a differentially-expressed gene in a pharmaceutical composition as described herein, to a subject in need of such treatment.

The following examples are offered by way of illustration and are not intended to be limiting.

EXAMPLES Genomic Determinants Of Cellular Drug Resistance And Treatment Response In Acute Lymphoblastic Leukemia I. Introduction

The present study was undertaken to identify genes that are differentially expressed in primary acute lymphoblastic leukemia cells that are sensitive or resistant to the widely used antileukemic agents: prednisolone, vincristine, L-asparaginase and daunorubicin, and to determine whether differential expression of these drug resistance genes influences treatment response. This study has revealed novel patterns of gene expression that confer cellular drug resistance and discriminate treatment outcome.

II. Methods A. Patients and Isolation of Leukemia Cells.

Pre-treatment bone marrow and peripheral blood were obtained after informed consent from children with newly diagnosed acute lymphoblastic leukemia who were enrolled on the ALL-IX Dutch Childhood Leukemia Study Group protocol at the ErasmusMC/Sophia Children's Hospital or on German Cooperative Study Group for Childhood Acute Lymphoblastic Leukemia COALL-92 and 97 treatment protocols (Harms et al. (2003) Blood 102:2736-2740). Mononuclear cells were isolated by sucrose density gradient centrifugation (Lymphoprep™, density 1.077 mg/ml; Nycomed Pharma), within 24 hours after sampling. Cells were re-suspended in culture medium consisting of RPMI 1640 (Dutch modification without L-glutamine; Gibco™) supplemented with 20 percent fetal calf serum (Integro), 2 mM L-glutamine, 200 μg/ml gentamycin (Gibco™) 100 IU/ml penicillin, 100 μg/ml streptomycin, 0.125 μg/ml fungizone (Gibco™), and 5 μg/ml insulin, 5 μg/ml transferrin and 5 ng/ml sodium selenite (ITS media supplement; Sigma-Aldrich Chemie B.V.). Where necessary, leukemic samples were further enriched to more than 90 percent leukemic blasts by removing non-malignant cells with immunomagnetic beads (DynaBeads®). The independent test set consists of patients with acute lymphoblastic leukemia treated on the St. Jude Children's Research Hospital Protocols Total Therapy XIIIA and B. Pui et al. (2003) JAMA 290:2001-7.

B. In Vitro Drug Resistance Assay.

Sensitivity of leukemia cells to prednisolone (Bufa Pharmaceutical Products), vincristine (TEVA Pharma), L-asparaginase (Paronal, Christiaens), and daunorubicin (Cerubidine, Rhône-Poulenc Rorer) was determined using the 4-day in vitro MTT drug resistance assay, as described in den Boer et al. (2003). J. Clin. Oncol. 21:3262-68. The ranges of concentrations tested were: prednisolone, 0.008-250 μg/ml; vincristine, 0.05-50 μg/ml; L-asparaginase, 0.003-10 IU/ml and daunorubicin, 0.002-2.0 μg/ml. The drug concentration lethal to 50 percent of the leukemia cells (LC50-value) was used as the measure of cellular drug resistance. The LC50-values used to assign cases as sensitive or resistant to each agent, were those previously associated with a good or bad treatment outcome in children with acute lymphoblastic leukemia. See, Table 1.

TABLE 1 LC₅₀ values for classification of resistant and sensitive ALL for each chemotherapeutic agent* Drug Sensitive Resistant Prednisolone ≦0.100 μg/ml   ≧150 μg/ml Vincristine ≦0.391 μg/ml ≧1.758 μg/ml L-asparaginase ≦0.033 IU/ml ≧0.912 IU/ml Daunorubicin ≦0.075 μg/ml ≧0.114 μg/ml *LC₅₀ by MTT as described by Pieters et al. (1991) Lancet 991:338:399-403. Classification based on LC₅₀ values previously associated with treatment outcome as described in den Boer et al. (2003) J. Clin. Oncol. 21: 3262-68.

C. RNA Purification, Labeling and Hybridization.

Total cellular RNA was extracted from a minimum of 5×106 leukemic cells using Trizol® reagent (Gibco™), RNA was additionally purified with phenol/chloroform/isoamylalcohol (25:24:1) and RNA integrity was assessed as described in Cheok et al. (2003) Nat. Genet. 34:85-90; and Yeoh et al. (2002) Cancer Cell 1:133-43. RNA processing and hybridization to the U133A GeneChip® oligonucleotide microarray (Affymetrix®) was performed according to manufacturer's protocol.

D. Data Analysis.

Gene expression values were calculated using Affymetrix® Microarray Suite (MAS) 5.0. 20,21. Expression signals were scaled to the target intensity of 2500 and log-transformed. Arrays were omitted if the scaling factor exceeded three standard deviations of the mean or if either the beta-actin or glyceraldehyde-3-phosphate dehydrogenase (GAPDH) 3′/5′ ratio was greater than three. From the total of 22,283 probe sets, those expressed in fewer than five patients were omitted, leaving 14,550 probe sets for subsequent analyses.

For each antileukemic agent, a significant number of genes that were most discriminative for resistant and sensitive leukemia samples were identified. A Wilcoxon rank sum test and t-test was applied for each probe set and the significance and false discovery rate was estimated using an empirical Bayesian approach, based on one thousand random permutations.

To determine the prediction accuracy using the top discriminating genes, the 173 acute lymphoblastic leukemia patients under study were randomly split into two groups, i.e. two thirds of the patients were used to build the model and the remaining one third to test the accuracy of the model. Prediction accuracy for each antileukemic agent and their confidence intervals were computed based on one thousand random splits using support vector machine as the classifier. In each random split, a gene expression score was assigned to each case in the test set (i.e., 1 if predicted to be sensitive, 2 if predicted to be resistant). The average gene expression score was computed for each patient for all four drugs using top 30, 50, and 100 gene probe sets. The combined drug resistance gene expression score for each patient was calculated as the sum of scores for each individual drug.

Gene expression scores used in the outcome analysis for the 173 Dutch and COALL patients and for the 98 patients 24 in the independent test set were also computed based on only the 172 gene probe sets discriminating sensitive versus resistant leukemia for each drug in the original cohort of patients, utilizing bootstrapping and support vector machine. For the analysis of disease-free survival, any type of leukemia relapse was considered. The duration of disease-free survival was defined as the time from diagnosis until the date of treatment failure. Time was censored at the last follow-up date if no failure was observed. Cox proportional hazard regression analysis was used to assess the association between combined gene expression score and treatment outcome. Leukemia-free survival was analyzed using Fine and Gray's estimator accounting for competing events.

Fisher's exact test was used to determine the over- or under-representation of discriminating genes in specific functional groups compared to the genes present on the U133A GeneChip®, using the Gene Ontology database (www.geneontology.org).

III. Results

Gene expression was determined in acute lymphoblastic leukemia cells from 173 newly diagnosed patients whose leukemia cells exhibited de novo sensitivity or resistance to a panel of four antileukemic agents, (i.e., prednisolone, vincristine, L-asparaginase and daunorubicin), as assessed in the in vitro MTT assay. The distribution of LC50-values in our study population did not differ from the entire population of 700 patients for whom we had determined sensitivity to each of these antileukemic agents. Likewise, the proportion of patients classified as “sensitive” or “resistant”, using previously defined LC50-values (Table 1) did not differ between the study group and the entire population.

A. Identification of Differentially Expressed Genes Using Supervised Learning Methods and Assessment of Prediction Accuracy.

Unsupervised hierarchical clustering, which groups patients based on predominant similarities in gene expression, did not cluster patients according to their resistance to any of the four antileukemic agents. Acute lymphoblastic leukemia patients were clustered predominately by immunophenotype. Because T-lineage acute lymphoblastic leukemia cases display a strong gene expression signature, subsequent analyses were performed using either (a) all samples or (b) only the B-lineage acute lymphoblastic leukemia samples. Analyses using only T-lineage ALL patients were not performed because the number of T-ALL cases was too small (n=28).

Supervised methods (i.e., Wilcoxon rank sum test and t-test) were used to build a gene-expression-based discrimination model to identify genes associated with either drug resistance or sensitivity. Selection of genes using either Wilcoxon rank sum test or t-test yielded similar results. Probe sets were rank-ordered according to their P-values, with the smallest P-values indicating the strongest statistical difference between resistant and sensitive patients. Permutation analyses of gene probe sets associated with resistance to prednisolone, vincristine and L-asparaginase gave a high overall significance (P<0.001) in both the total population and within the B-lineage group (Table 2), whereas gene probe sets associated with daunorubicin resistance were significant (P=0.001) in the B-lineage group, but not at the P=0.05 level in the total group. In concordance, the false discovery rate was higher in daunorubicin compared to the other three drugs. For all drugs, the false discovery rates were lower in the B-lineage group compared to the total group (Table 2). Using the top 30, 50 and 100 discriminating genes for each drug, prediction accuracies were 67 to 73 percent, with P-values of 0.007 to 0.045 (Table 3). Within the cohort of patients with B-lineage acute lymphoblastic leukemia, the estimated prediction accuracies were even higher, ranging from 71 to 76 percent, with P-values ranging from 0.004 to 0.025. Multiple logistic regression analysis indicated that gene expression profiles were a significant predictor of drug resistance for all four drugs, independent of known prognostic factors (i.e., age and white blood cell count; Table 4).

TABLE 2a Patient Permutation analysis and false discovery rate: All patients* α = 0.0001 α = 0.0005 α = 0.001 P- P- P- Drug n FDR (%) value n FDR (%) value N FDR (%) value PRED 11 10 <0.001 32 15 <0.001 53 22 <0.001 VCR 7 12 <0.001 76 14 <0.001 76 14 <0.001 ASP 24 5 <0.001 91 6 <0.001 135 9 <0.001 DNR 2 42 0.06 11 49 0.1 27 44 0.07

TABLE 2b Patient Permutation analysis and false discovery rate: B-lineage patients* α = 0.0001 α = 0.0005 α = 0.001 P- P- P- Drug n FDR (%) value n FDR (%) value N FDR (%) value PRED 19 6 <0.001 57 8 <0.001 92 13 <0.001 VCR 22 5 <0.001 74 8 <0.001 138 10 <0.001 ASP 67 2 <0.001 202 3 <0.001 279 4 <0.001 DNR 5 15 <0.001 25 21 0.001 38 32 0.001 *Permutation analysis (n = 1000) was computed for each dataset (prednisolone (PRED), vincristine (VCR), L-asparaginase (ASP), daunorubicin (DNR) using (a) all patients and (b) only patients with B-lineage acute lymphoblastic leukemia. For each P-value using Wilcoxon rank sum rank test (α), the number of probe sets (n), the false discovery rate (FDR) and the overall significance (P-value) are listed. In each random permutation, the class label (resistant or sensitive) was randomly assigned to each patient and genes were reselected using Wilcoxon rank sum test and t-test based on the random labels. The overall significance (P α) of the model was estimated using the following formula: P_(α = (n permutations with N) _(α) ^(random) ≧ N_(α) ^(obs))/(Total n of permutations) Where α is the P-value using Wilcoxon rank sum test and t-test; N_(α) ^(random) is the number of probe sets with P-values less than a using random class label; N_(α) ^(obs) is the number of probe sets with P-values less than α using the observed class label. The false discovery rate (FDR_(α) was estimated as: FDR_(α) = (median(N_(α) ^(random)))N_(α) ^(obs) Principal component analysis and 2D-hierarchical clustering were performed using GeneMaths ™ 2.1 software (AppliedMaths, St. Martens-Latem, Belgium). To show that discriminating genes were not obtained by chance, the significance and false discovery rate was estimated using an empirical Bayesian approach based on one thousand permutations. The top principal components based on top-ranked probe sets (30, 50 or 100) re-selected by Wilcoxon rank sum test were used to construct support vector machines as prediction models. Statistical significance of the prediction accuracy compared to chance (50 percent accuracy) was determined by permutation analyses.

TABLE 3a Patient prediction accuracy using gene expression profiles for classification of drug resistant and sensitive acute lymphoblastic leukemia: All patients* n accuracy (%) 95% C.I. P-value PRED 30 71 58-81 0.031 50 71 58-81 0.031 100 71 58-81 0.031 VCR 30 68 59-78 0.029 50 71 59-79 0.012 100 71 59-79 0.012 ASP 30 67 53-76 0.045 50 67 52-79 0.045 100 67 55-78 0.045 DNR 30 73 60-80 0.007 50 73 60-80 0.007 100 73 58-76 0.007

TABLE 3b Patient prediction accuracy using gene expression profiles for classification of drug resistant and sensitive acute lymphoblastic leukemia: B-lineage patients* n accuracy (%) 95% C.I. P-value PRED 30 75 63-88 0.025 50 75 63-88 0.025 100 75 67-87 0.025 VCR 30 74 62-85 0.010 50 76 62-85 0.004 100 76 62-85 0.004 ASP 30 71 60-83 0.018 50 71 57-83 0.018 100 71 60-80 0.019 DNR 30 76 65-85 0.004 50 76 65-85 0.004 100 76 67-84 0.004 *Patient Prediction accuracy using gene expression profiles for classification of drug resistant and sensitive acute lymphoblastic leukemia. Prediction accuracy for each antileukemic agent using 30, 50 or 100 probe sets. The median prediction accuracy is shown with corresponding P-values and the 95 percent confidence interval (C.I.) for prednisolone (PRED), vincristine (VCR), L-asparaginase (ASP) and daunorubicin (DNR) (a) based on all patients and (b) for only patients with B-lineage acute lymphoblastic leukemia.

TABLE 4 Multivariate analysis of gene expression and known prognostic factors (age, WBC count) to discriminate drug resistance* Odds ratio Predictor (95% C.I.) P-value PRED gene expression score 57.8 (4.9-681.6) 0.001 age (years) 1.17 (1.01-1.36) 0.038 WBC count (10⁹/L) 1.0 (0.98-1.01) 0.427 VCR gene expression score 13.5 (1.97-92.6) 0.008 age (years) 1.0 (0.89-1.13) 0.995 WBC count (10⁹/L) 0.99 (0.99-1.0) 0.084 ASP gene expression score 22.1 (4.8-102.6) <0.001 age (years) 1.13 (1.01-1.26) 0.033 WBC count (10⁹/L) 1.0 (0.99-1.01) 0.792 DNR gene expression score 151.2 (4.1-5533.6) 0.006 age (years) 1.04 (0.93-1.17) 0.455 WBC count (10⁹/L) 1.0 (0.99-1.0) 0.273 *Multiple logistic regression was used with gene expression and known prognostic factors (age, WBC count) to discriminate drug resistance.

Gene expression scores were also computed for the patients with intermediate drug sensitivity (Table 5), revealing median scores that were between the median gene expression score of the drug sensitive and drug resistant groups for all four antileukemic agents. For L-asparaginase and prednisolone, the gene expression scores of the intermediate group were significantly different from both the sensitive group and the resistant group (P<0.05, Wilcoxon rank sum test). For daunorubicin and vincristine, the intermediate group was significantly different from the sensitive group, but not from the resistant group (Table 5).

TABLE 5 Gene expression scores for the intermediate sensitivity group, using genes selected to discriminate resistant and sensitive B-lineage ALL* resistant intermediate n (R) (I) sensitive (S) R vs. S R vs. I I vs. S PRED 50 1.28 1.04 1.02 <0.001 0.002 0.044 (1.01-1.96) (1.0-1.88) (1.0-1.65) 100 1.29 1.01 1.01 <0.001 0.001 0.035 (1.01-1.99) (1.0-1.92) (1.0-1.72) VCR 50 1.29 1.29 1.11 0.006 0.659 0.002 (1.01-1.88) (1.01-1.61)  (1.01-1.9)  100 1.26 1.24 1.08 0.002 0.518 0.002 (1.01-1.93) (1.0-1.68) (1.0-1.94) ASP 50 1.53 1.31 1.14 <0.001 0.013 0.004 (1.03-1.91) (1.02-1.88)  (1.01-1.97)  100 1.51 1.31 1.1  <0.001 0.024 0.008 (1.02-1.91) (1.0-1.92) (1.0-1.98) DNR 50 1.16 1.11 1.04 0.021 0.404 0.090 (1.0-1.5) (1.0-1.71) (1.0-1.6)  100 1.15 1.07 1.01 0.019 0.583 0.045  (1.0-1.47) (1.0-1.81) (1.0-1.56) *Gene expression scores for the intermediate sensitivity group, using genes selected to discriminate resistant and sensitive B-lineage ALL. The resistant and sensitive patients were randomly split into ⅔ training set and ⅓ test set. Additionally, all intermediate patients were included in the test set. A patient in the test set was assigned a score of 1 if classified by the model as sensitive and 2 if resistant; no score was assigned to patients in the training set. The above was repeated 1000 times to compute a gene expression score for each patient as the average of scores ever assigned to the patient. Median gene expression scores of resistant (R), sensitive (S) and intermediate (I) samples as well as the range in parentheses are presented based on 50 and 100 probe sets. The P-values are given for each pair wise comparison, using Wilcoxon rank sum test.

B. Supervised Clustering and Principal Component Analysis.

The number of genes used to build the drug resistance model for each antileukemic agent was determined based upon the false discovery rate, permutation analysis and prediction accuracy for all patients (Table 2). This identified 172 probe sets corresponding to 123 unique gene annotations and 30 cDNA clones (some genes are represented on the array by multiple probe sets), that were differentially expressed in sensitive and resistant B-lineage acute lymphoblastic leukemia. Hierarchical clustering using the selected probe sets correctly assigned 66 of 74 cases for prednisolone (89 percent apparent accuracy), 84 of 104 for vincristine (81 percent), 83 of 106 for L-asparaginase (78 percent) and 86 of 105 for daunorubicin (82 percent). Similarly, principal component analyses correctly grouped the majority of patients into either the resistant cluster or the sensitive cluster for each of the four antileukemic agents. Hierarchical clustering and principal component analyses of all patients gave similar results. The probe set ID, gene names, annotations and the gene expression ratio for resistant versus sensitive leukemia for discriminating genes are shown for each drug in Tables 6-9 (B-lineage acute lymphoblastic leukemia) and Tables 10-13 (B- and T-lineage acute lymphoblastic leukemia).

TABLE 6A Top genes discriminating prednisolone resistant and sensitive B- lineage ALL: Genes down-regulated in prednisolone resistant B-lineage ALL NCBI R/S Accession Probe ID Gene Name Gene Symbol ratio Number 208660_at citrate synthase CS 0.82 BC000105 201896_s_at CDC28 protein kinase CKS1B 0.39 BC001425 regulatory subunit 1B 209675_s_at E1B-55 kDa-associated protein 5 E1B-AP5 0.70 BC004242 217729_s_at amino-terminal enhancer AES 0.60 NM_001130 of split 209760_at KIAA0922 protein KIAA0922 0.65 AL136932 202521_at CCCTC-binding factor CTCF 0.67 NM_006565 (zinc finger protein) 212167_s_at SWI/SNF related, matrix SMARCB1 0.76 AK021419 associated, actin dependent regulator 201938_at CDK2-associated protein 1 CDK2AP1 0.47 NM_004642 216484_x_at hepatoma-derived HDGF 0.71 L24521 growth factor (high- mobility group protein 1-1 200896_x_at hepatoma-derived HDGF 0.70 NM_004494 growth factor (high- mobility group protein 1-1 38710_at ubiquitin-specific FLJ20113 0.79 AL096714 protease otubain 1 212100_s_at KIAA1649 protein KIAA1649 0.71 Z93241 219679_s_at WW domain-containing WAC 0.69 NM_018604 adapter with a coiled-coil region 221547_at PRP18 pre-mRNA PRPF18 0.72 BC000794 processing factor 18 homolog (yeast) 217978_s_at NICE-5 protein HSA243666 0.77 NM_017582 213061_s_at hypothetical protein LOC123803 0.59 AA643304 LOC123803 208766_s_at heterogeneous nuclear R HNRPR 0.82 BC001449 ribonucleoprotein 212910_at HRIHFB2206 protein HRIHFB2206 0.54 W19873 47083_at hypothetical protein MGC2718 0.81 AI280108 MGC2718 208781_x_at sorting nexin 3 SNX3 0.77 AF062483 218438_s_at endothelial-derived gene 1 EG1 0.76 NM_025205 208620_at poly(rC) binding protein 1 PCBP1 0.67 U24223 203274_at coagulation factor VIII- F8A 0.51 NM_012151 associated (intronic transcript) 208739_x_at SMT3 suppressor of mif SMT3H2 0.69 L76416 two 3 homolog 2 (yeast)

TABLE 6B Top genes discriminating prednisolone resistant and sensitive B- lineage ALL: Genes up-regulated in prednisolone resistant ALL NCBI R/S Accession Probe ID Gene Name Gene Symbol ratio Number 206209_s_at carbonic anhydrase IV CA4 1.56 NM_000717 208205_at protocadherin alpha 9 PCDHA9 1.63 NM_014005 206905_s_at matrilin 1, cartilage matrix protein MATN1 2.04 NM_002379 207452_s_at contactin 5 CNTN5 1.58 NM_014361 212581_x_at glyceraldehyde-3- GAPD 1.25 BE561479 phosphate dehydrogenase 217398_x_at glyceraldehyde-3- GAPD 1.37 AK026525 phosphate dehydrogenase AFFX- glyceraldehyde-3- GAPD 1.21 M33197 HUMGAP phosphate dehydrogenase AFFX- glyceraldehyde-3- GAPD 1.20 M33197 HUMGAP phosphate dehydrogenase 213453_x_at glyceraldehyde-3- GAPD 1.26 BF689355 phosphate dehydrogenase 214057_at myeloid cell leukemia MCL1 1.72 H71805 sequence 1 (BCL2- related) 203149_at poliovirus receptor- PVRL2 2.01 NM_002856 related 2 (herpesvirus entry mediator B) 222088_s_at solute carrier family 2 SLC2A14 2.07 AA778684 (facilitated glucose transporter) 205193_at v-maf MAFF 1.69 NM_012323 musculoaponeurotic fibrosarcoma oncogene homolog F 36711_at v-maf MAFF 2.06 AL021977 musculoaponeurotic fibrosarcoma oncogene homolog F 202201_at biliverdin reductase B BLVRB 2.31 NM_000713 (flavin reductase (NADPH)) 201061_s_at stomatin STOM 1.84 M81635 218589_at purinergic receptor P2RY5 2.91 NM_005767 P2Y, G-protein coupled, 5 209795_at CD69 antigen (p60, CD69 2.26 L07555 early T-cell activation antigen)

TABLE 6C Genes discriminating prednisolone resistant and sensitive B- lineage ALL to the 0.001 < p < 0.01 level by both T-test and Wilcoxon: Genes down-regulated in prednisolone resistant B-lineage ALL NCBI Accession Gene Number Gene Name Symbol NM_013299 protein predicted by clone 23627 HSU79266 U84138 RAD51-like 1 (S. cerevisiae) RAD51L1 NM_005679 “TATA box binding protein (TBP)-associated TAF1C factor, RNA polymerase I, C, 110 kDa” AL582836 paternally expressed 10 PEG10 AF277194 putative membrane protein LOC54499 BC000229 hypothetical protein MGC2488 MGC2488 NM_022149 MAGEF1 protein MAGEF1 AL536319 KIAA0993 protein KIAA0993 NM_004190 “lipase, gastric” LIPF NM_014292 chromobox homolog 6 CBX6 BC001425 p53-regulated DDA3 DDA3 NM_001431 erythrocyte membrane protein band 4.1-like 2 EPB41L2 AF068220 “ATPase, Ca++ transporting, ubiquitous” ATP2A3 NM_016553 nucleoporin 62 kDa NUP62 AW299740 dihydrolipoamide S-acetyltransferase (E2 DLAT component of pyruvate dehydrogenase complex) U49396 “purinergic receptor P2X, ligand-gated ion P2RX5 channel, 5” NM_000465 BRCA1 associated RING domain 1 BARD1 AK001327 Tax interaction protein 1 TIP-1 NM_018036 hypothetical protein FLJ10242 FLJ10242 NM_016256 N-acetylglucosamine-1-phosphodiester alpha- LOC51172 N-acetylglucosaminidase NM_006806 “BTG family, member 3” BTG3 AF257659 calumenin CALU NM_017920 up-regulated gene 4 URG4 NM_002383 MYC-associated zinc finger protein (purine- MAZ binding transcription factor) NM_021212 HCF-binding transcription factor Zhangfei ZF AK026607 p53-induced protein PIG11 NM_014345 endocrine regulator HRIHFB2436 AW450363 ADP-ribosylation factor-like 7 ARL7 AL110206 Homo sapiens mRNA; cDNA DKFZp586N2022 (from clone DKFZp586N2022) BF677486 “thymosin, beta, identified in neuroblastoma TMSNB cells” AW138827 “TAF5 RNA polymerase II, TATA box TAF5 binding protein (TBP)-associated factor, 100 kDa” NM_024067 hypothetical protein MGC2718 MGC2718 BF576458 nuclear receptor coactivator 1 NCOA1 BE646618 mitogen-activated protein kinase kinase MAP4K1 kinase kinase 1 AK026682 “Homo sapiens cDNA: FLJ23029 fis, clone LNG01883” NM_004053 bystin-like BYSL NM_018095 hypothetical protein FLJ10450 FLJ10450 W19873 HRIHFB2206 protein HRIHFB2206 X17115 immunoglobulin heavy constant mu IGHM AI858004 immunoglobulin heavy constant gamma 3 IGHG3 (G3m marker) AF312918 Mlx interactor MONDOA AW270932 hypothetical protein FLJ20275 FLJ20275 AI800983 “cleavage and polyadenylation specific factor CPSF5 5, 25 kDa” NM_025104 Dbf4-related factor 1 DRF1 NM_004642 CDK2-associated protein 1 CDK2AP1 NM_014736 KIAA0101 gene product KIAA0101 NM_014322 “opsin 3 (encephalopsin, panopsin)” OPN3 AA877910 “ATPase, Ca++ transporting, ubiquitous” ATP2A3 NM_021992 “thymosin, beta, identified in neuroblastoma TMSNB cells” NM_012151 coagulation factor VIII-associated (intronic F8A transcript) NM_000626 CD79B antigen (immunoglobulin-associated CD79B beta) NM_014791 maternal embryonic leucine zipper kinase MELK BF510692 paired box gene 5 (B-cell lineage specific PAX5 activator protein) AA643304 Homo sapiens mRNA; cDNA DKFZp666E058 (from clone DKFZp666E058) BG391171 thymopoietin TMPO NM_002358 MAD2 mitotic arrest deficient-like 1 (yeast) MAD2L1 AV682679 selenium donor protein SPS J04977 “X-ray repair complementing defective repair XRCC5 in Chinese hamster cells 5 (double-strand- break rejoining; Ku autoantigen, 80 kDa)” AB014562 KIAA0662 gene product KIAA0662 M18003 ferredoxin 1 FDX1 AK000993 “Homo sapiens cDNA FLJ10131 fis, clone HEMBA1003041” NM_005173 “ATPase, Ca++ transporting, ubiquitous” ATP2A3 AF151853 preimplantation protein 3 PREI3 NM_021813 “BTB and CNC homology 1, basic leucine BACH2 zipper transcription factor 2” BF340123 hypothetical protein FLJ11149 FLJ11149 NM_004111 flap structure-specific endonuclease 1 FEN1 BE964689 ubiquitin-conjugating enzyme E2L 3 UBE2L3 BF432873 “proteasome (prosome, macropain) 26S PSMD11 subunit, non-ATPase, 11” BF034561 G-rich RNA sequence binding factor 1 GRSF1 NM_005663 Wolf-Hirschhorn syndrome candidate 2 WHSC2 NM_007275 lung cancer candidate FUS1 AW272611 thymopoietin TMPO NM_017980 LIM and senescent cell antigen-like domains 2 LIMS2 AF231056 “SWI/SNF related, matrix associated, actin SMARCF1 dependent regulator of chromatin, subfamily f, member 1” AL137673 Homo sapiens mRNA; cDNA DKFZp434H0872 (from clone DKFZp434H0872) NM_023941 hypothetical protein MGC3032 MGC3032 NM_004450 enhancer of rudimentary homolog ERH (Drosophila) NM_002466 v-myb myeloblastosis viral oncogene MYBL2 homolog (avian)-like 2 BF001666 Homo sapiens clone 23870 mRNA sequence NM_001938 “down-regulator of transcription 1, TBP- DR1 binding (negative cofactor 2)” BC004439 translocase of inner mitochondrial membrane TIMM17A 17 homolog A (yeast) Y15724 “ATPase, Ca++ transporting, ubiquitous” ATP2A3 NM_001130 amino-terminal enhancer of split AES AW612574 lecuine-rich acidic protein-like protein LANP-L NM_016200 U6 snRNA-associated Sm-like protein LSm8 LOC51691 BG338532 SMT3 suppressor of mif two 3 homolog 1 SMT3H1 (yeast) AB011093 Rho-specific guanine nucleotide exchange P114-RHO- factor p114 GEF AB018305 “spondin 1, (f-spondin) extracellular matrix SPON1 protein” AF035737 “general transcription factor II, i” GTF2I AL515874 “Homo sapiens cDNA FLJ33806 fis, clone CTONG2000846” NM_021940 stromal membrane-associated protein SMAP1 NM_003372 von Hippel-Lindau binding protein 1 VBP1 AA195999 mitogen-activated protein kinase 1 MAPK1 NM_024649 hypothetical protein FLJ23590 FLJ23590 NM_003685 KH-type splicing regulatory protein (FUSE KHSRP binding protein 2) AL136932 KIAA0922 protein KIAA0922 BC004273 “splicing factor 3b, subunit 4, 49 kDa” SF3B4 BG528818 pre-mRNA splicing factor 17 PRP17 AF267865 DKFZP564A043 protein DKFZP564A043 NM_002979 sterol carrier protein 2 SCP2 NM_006577 “UDP-GlcNAc:betaGal beta-1,3-N- B3GNT1 acetylglucosaminyltransferase 1” NM_001783 CD79A antigen (immunoglobulin-associated CD79A alpha) AI936769 “FK506 binding protein 1A, 12 kDa” FKBP1A L21990 “splicing factor 3a, subunit 2, 66 kDa” SF3A2 U76248 seven in absentia homolog 2 (Drosophila) SIAH2 AF101434 Wolf-Hirschhorn syndrome candidate 2 WHSC2 NM_006565 CCCTC-binding factor (zinc finger protein) CTCF AF217963 “melanoma antigen, family D, 1” MAGED1 AV756141 “colony stimulating factor 2 receptor, beta, CSF2RB low-affinity (granulocyte-macrophage)” AF234997 Tax interaction protein 1 TIP-1 NM_012394 prefoldin 2 PFDN2 NM_018604 WW domain-containing adapter with a WAC coiled-coil region M19156 keratin 10 (epidermolytic hyperkeratosis; KRT10 keratosis palmaris et plantaris) AI478300 “ESTs, Weakly similar to neuronal thread protein [Homo sapiens] [H. sapiens]” NM_015895 “geminin, DNA replication inhibitor” GMNN U20498 “cyclin-dependent kinase inhibitor 2D (p19, CDKN2D inhibits CDK4)” Z25435 BC005338 “capping protein (actin filament) muscle Z- CAPZA2 line, alpha 2” BC003376 “ELAV (embryonic lethal, abnormal vision, ELAVL1 Drosophila)-like 1 (Hu antigen R)” NM_004759 mitogen-activated protein kinase-activated MAPKAPK2 protein kinase 2 BC000903 high-mobility group box 2 HMGB2 BC004242 E1B-55 kDa-associated protein 5 E1B-AP5 NM_013387 ubiquinol-cytochrome c reductase complex HSPC051 (7.2 kD) NM_000801 “FK506 binding protein 1A, 12 kDa” FKBP1A NM_003133 signal recognition particle 9 kDa SRP9 NM_024299 chromosome 20 open reading frame 149 C20orf149 AI744900 “SWI/SNF related, matrix associated, actin SMARCA4 dependent regulator of chromatin, subfamily a, member 4” NM_024644 hypothetical protein FLJ21802 FLJ21802 AI589507 hypothetical protein MGC5466 MGC5466 NM_016640 mitochondrial ribosomal protein S30 MRPS30 AK026120 KIAA0460 protein KIAA0460 NM_015955 C21orf19-like protein LOC51072 NM_021183 “hypothetical protein similar to small G LOC57826 proteins, especially RAP-2A” BC000794 PRP18 pre-mRNA processing factor 18 PRPF18 homolog (yeast) NM_014045 low density lipoprotein receptor-related LRP10 protein 10 AK000311 Homo sapiens mRNA; cDNA DKFZp564E2222 (from clone DKFZp564E2222) NM_021183 “hypothetical protein similar to small G LOC57826 proteins, especially RAP-2A” NM_021242 hypothetical protein STRAIT11499 STRAIT11499 M25269 “ELK1, member of ETS oncogene family” ELK1 NM_007146 zinc finger protein 161 ZNF161 AF067173 “mago-nashi homolog, proliferation- MAGOH associated (Drosophila)” NM_005826 heterogeneous nuclear ribonucleoprotein R HNRPR D26156 “SWI/SNF related, matrix associated, actin SMARCA4 dependent regulator of chromatin, subfamily a, member 4” U24223 poly(rC) binding protein 1 PCBP1 BC004913 papillary renal cell carcinoma (translocation- PRCC associated) NM_006333 nuclear DNA-binding protein C1D NM_018221 chromosome 2 open reading frame 6 C2orf6 AF141304 “RAB5C, member RAS oncogene family” RAB5C NM_014820 translocase of outer mitochondrial membrane TOMM70A 70 homolog A (yeast) D63882 “DMC1 dosage suppressor of mck1 homolog, DMC1 meiosis-specific homologous recombination (yeast)” NM_014165 HSPC125 protein HSPC125 NM_003094 small nuclear ribonucleoprotein polypeptide E SNRPE BC002809 “down-regulator of transcription 1, TBP- DR1 binding (negative cofactor 2)” AL134724 Homo sapiens clone 24711 mRNA sequence L24521 “Human transformation-related protein mRNA, 3′ end” AA586774 “serine/threonine kinase 24 (STE20 homolog, STK24 yeast)” L20817 “discoidin domain receptor family, member DDR1 1” NM_015343 likely ortholog of Xenopus dullard HSA011916 U82819 “uncoupling protein 2 (mitochondrial, proton UCP2 carrier)” NM_002208 “integrin, alpha E (antigen CD103, human ITGAE mucosal lymphocyte antigen 1; alpha polypeptide)” Z93241 hypothetical protein DKFZP434G0310 DKFZP434G0310 AI363375 hypothetical protein BC002926 LOC90379 NM_004494 hepatoma-derived growth factor (high- HDGF mobility group protein 1-like) NM_005496 SMC4 structural maintenance of SMC4L1 chromosomes 4-like 1 (yeast) NM_014628 gene predicted from cDNA with a complete KIAA0110 coding sequence NM_006402 hepatitis B virus x interacting protein HBXIP NM_014837 chromosome 1 open reading frame 16 C1orf16 L76416 SMT3 suppressor of mif two 3 homolog 2 SMT3H2 (yeast) AI741124 “guanine nucleotide binding protein (G GNB1 protein), beta polypeptide 1” NM_006559 “KH domain containing, RNA binding, signal KHDRBS1 transduction associated 1” AW516932 “down-regulator of transcription 1, TBP- DR1 binding (negative cofactor 2)” NM_007373 soc-2 suppressor of clear homolog (C. elegans) SHOC2 NM_014403 “sialyltransferase 7D ((alpha-N- SIAT7D acetylneuraminyl-2,3-beta-galactosyl-1,3)-N- acetyl galactosaminide alpha-2,6- sialyltransferase)” NM_014225 “protein phosphatase 2 (formerly 2A), PPP2R1A regulatory subunit A (PR 65), alpha isoform” AD001527 cytoskeleton-associated protein 1 CKAP1 NM_006388 “HIV-1 Tat interactive protein, 60 kDa” HTATIP BC005147 “FK506 binding protein 1A, 12 kDa” FKBP1A NM_025205 endothelial-derived gene 1 EG1 BC005212 hypothetical protein FLJ20003 FLJ20003 NM_004622 translin TSN AI471665 MYC-associated zinc finger protein (purine- MAZ binding transcription factor) AK021419 “SWI/SNF related, matrix associated, actin SMARCB1 dependent regulator of chromatin, subfamily b, member 1” AK022555 KIAA0618 gene product KIAA0618 AA534860 histone H2A.F/Z variant H2AV NM_031298 hypothetical protein MGC2963 MGC2963 NM_007234 dynactin 3 (p22) DCTN3 BC005876 “ATPase, H+ transporting, lysosomal 21 kDa, ATP6V0B V0 subunit c”” NM_003173 suppressor of variegation 3-9 homolog 1 SUV39H1 (Drosophila) NM_006826 “tyrosine 3-monooxygenase/tryptophan 5- YWHAQ monooxygenase activation protein, theta polypeptide” NM_007279 U2 small nuclear ribonucleoprotein auxiliary U2AF65 factor (65 kD) AF067173 “mago-nashi homolog, proliferation- MAGOH associated (Drosophila)” NM_017582 NICE-5 protein HSA243666 BF675004 “poly(A) binding protein, nuclear 1” PABPN1 NM_015485 DKFZP566K023 protein DKFZP566K023 AF062483 sorting nexin 3 SNX3 AI679080 “SWI/SNF related, matrix associated, actin SMARCF1 dependent regulator of chromatin, subfamily f, member 1” NM_003769 “splicing factor, arginine/serine-rich 9” SFRS9 NM_002074 “guanine nucleotide binding protein (G GNB1 protein), beta polypeptide 1” AW139179 fem-1 homolog b (C. elegans) FEM1B AL096714 hypothetical protein FLJ20113 FLJ20113 AI280108 hypothetical protein MGC2718 MGC2718 W93787 “golgi reassembly stacking protein 2, 55 kDa” GORASP2 NM_005334 host cell factor C1 (VP16-accessory protein) HCFC1 NM_006842 “splicing factor 3b, subunit 2, 145 kDa” SF3B2 AL031133 “ESTs, Highly similar to SM32_HUMAN Ubiquitin-like protein SMT3B (Sentrin 2) [H. sapiens]” BE748755 “chromobox homolog 3 (HP1 gamma CBX3 homolog, Drosophila)” BC004239 jumping translocation breakpoint JTB BC000105 citrate synthase CS BC001449 heterogeneous nuclear ribonucleoprotein R HNRPR AB047360 sorting nexin 3 SNX3 NM_005877 “splicing factor 3a, subunit 1, 120 kDa” SF3A1 AF135162 cyclin I CCNI AF141349 hypothetical protein DKFZp434N0650 DKFZp434N0650 NM_006694 jumping translocation breakpoint JTB D80006 disco-interacting protein 2 (Drosophila) DIP2 homolog AW873564 “ESTs, Weakly similar to YHS1_YEAST HYPOTHETICAL 21.3 KD PROTEIN IN MSH1-EPT1 INTERGENIC REGION [S. cerevisiae]”

TABLE 6D Genes discriminating prednisolone resistant and sensitive B- lineage ALL to the 0.001 < p < 0.01 level by both T-test and Wilcoxon: Genes up-regulated in prednisolone resistant B-lineage ALL NCBI Accession Number Gene Name Gene Symbol NM_018955 ubiquitin B UBB AA349595 KIAA1091 protein KIAA1091 NM_017627 hypothetical protein FLJ20030 FLJ20030 NM_001006 ribosomal protein S3A RPS3A BF184532 ribosomal protein S20 RPS20 M33197 glyceraldehyde-3-phosphate dehydrogenase GAPD BC001019 ribosomal protein L39 RPL39 M33197 glyceraldehyde-3-phosphate dehydrogenase GAPD M33197 glyceraldehyde-3-phosphate dehydrogenase GAPD AA789278 ribosomal protein L13 RPL13 AW574664 ribosomal protein L13 RPL13 BE561479 glyceraldehyde-3-phosphate dehydrogenase GAPD BF689355 glyceraldehyde-3-phosphate dehydrogenase GAPD BC004954 ribosomal protein L13 RPL13 NM_004834 mitogen-activated protein kinase kinase MAP4K4 kinase kinase 4 AI186735 ribosomal protein L13 RPL13 NM_024305 hypothetical protein MGC4278 MGC4278 NM_005731 “actin related protein 2/3 complex, subunit 2, ARPC2 34 kDa” NM_000982 ribosomal protein L21 RPL21 BC006325 G-2 and S-phase expressed 1 GTSE1 AA927664 “transcription elongation factor B (SIII), TCEB1L polypeptide 1-like” AK026525 glyceraldehyde-3-phosphate dehydrogenase GAPD NM_014128 “ferritin, light polypeptide” FTL NM_017624 hypothetical protein FLJ20019 FLJ20019 NM_002870 “RAB13, member RAS oncogene family” RAB13 AL535380 “B-cell translocation gene 1, anti- BTG1 proliferative” AF022991 period homolog 1 (Drosophila) PER1 U36764 “eukaryotic translation initiation factor 3, EIF3S2 subunit 2 beta, 36 kDa” NM_018946 N-acetylneuraminic acid phosphate synthase; SAS sialic acid synthase AI889513 Homo sapiens mRNA; cDNA DKFZp686D1577 (from clone DKFZp686D1577) AI201594 Homo sapiens mRNA; cDNA DKFZp762M127 (from clone DKFZp762M127) AF064824 receptor-interacting serine-threonine kinase 2 RIPK2 BG537190 “ESTs, Highly similar to FRIL_HUMAN Ferritin light chain (Ferritin L subunit) [H. sapiens]” AV741657 “Homo sapiens cDNA: FLJ21692 fis, clone COL09588” AK000773 “Homo sapiens cDNA FLJ20766 fis, clone COL07978” AA872727 farnesyl-diphosphate farnesyltransferase 1 FDFT1 AW276522 “solute carrier family 6 (neurotransmitter SLC6A8 transporter, creatine), member 8” NM_025208 spinal cord-derived growth factor-B SCDGF-B NM_001530 “hypoxia-inducible factor 1, alpha subunit HIF1A (basic helix-loop-helix transcription factor)” AI275690 myeloid cell leukemia sequence 1 (BCL2- MCL1 related) NM_018370 hypothetical protein FLJ11259 FLJ11259 BG538564 “ferritin, light polypeptide” FTL NM_030978 “hypothetical protein similar to actin related MGC3038 protein 2/3 complex, subunit 5” AW003091 “Homo sapiens cDNA FLJ38849 fis, clone MESAN2008936” NM_016516 tumor antigen SLP-8p HCC8 AA191576 “nucleophosmin (nucleolar phosphoprotein NPM1 B23, numatrin)” U27336 “fucosyltransferase 6 (alpha (1,3) FUT6 fucosyltransferase)” AI378044 UDP-glucose ceramide glucosyltransferase UGCG NM_001273 chromodomain helicase DNA binding protein 4 CHD4 AA634272 signal transducer and activator of STAT3 transcription 3 (acute-phase response factor) NM_015367 MIL1 protein MIL1 AA443762 “guanine nucleotide binding protein (G GNB2L1 protein), beta polypeptide 2-like 1” S81916 “Phosphoglycerate kinase {alternatively spliced} [human, phosphoglycerate kinase deficient patient with episodes of muscl, mRNA Partial Mutant, 307 nt]” AF125393 “RAB27A, member RAS oncogene family” RAB27A NM_001455 forkhead box O3A FOXO3A NM_004604 syntaxin 4A (placental) STX4A AI819238 “inhibitor of DNA binding 2, dominant ID2 negative helix-loop-helix protein” NM_014349 “apolipoprotein L, 3” APOL3 NM_001616 “activin A receptor, type II” ACVR2 AU144792 “Homo sapiens cDNA FLJ10127 fis, clone HEMBA1002973, moderately similar to CAMP-DEPENDENT 3′,5′-CYCLIC PHOSPHODIESTERASE 4B (EC 3.1.4.17)” AI537887 erythrocyte membrane protein band 7.2 EPB72 (stomatin) L76666 “killer cell immunoglobulin-like receptor, KIR3DL2 three domains, long cytoplasmic tail, 2” NM_001759 cyclin D2 CCND2 L32185 “solute carrier family 11 (proton-coupled SLC11A1 divalent metal ion transporters), member 1” BC005043 hypothetical protein MGC31957 MGC31957 AW173157 Homo sapiens mRNA; cDNA DKFZp586G1922 (from clone DKFZp586G1922) N21202 “Homo sapiens cDNA FLJ35517 fis, clone SPLEN2000698” AB030824 Kruppel-like factor 5 (intestinal) KLF5 AL564683 “CCAAT/enhancer binding protein (C/EBP), CEBPB beta” H93077 chromosome 5 open reading frame 4 C5orf4 BC001120 “lectin, galactoside-binding, soluble, 3 LGALS3 (galectin 3)” M34428 “Pvt1 oncogene homolog, MYC activator PVT1 (mouse)” NM_012323 v-maf musculoaponeurotic fibrosarcoma MAFF oncogene homolog F (avian) NM_014918 carbohydrate (chondroitin) synthase 1 CHSY1 AU150691 “Homo sapiens cDNA FLJ10577 fis, clone NT2RP2003367” NM_005565 lymphocyte cytosolic protein 2 (SH2 domain LCP2 containing leukocyte protein of 76 kDa) NM_004720 “endothelial differentiation, lysophosphatidic EDG4 acid G-protein-coupled receptor, 4” N25732 forkhead box O3A FOXO3A N26005 “protein phosphatase 1, regulatory (inhibitor) PPP1R3C subunit 3C” NM_002970 spermidine/spermine N1-acetyltransferase SAT AL039469 exosome component Rrp41 FLJ20591 AL110298 “solute carrier family 2 (facilitated glucose SLC2A3 transporter), member 3” U62733 “carnitine palmitoyltransferase I, muscle” CPT1B NM_000717 carbonic anhydrase IV CA4 AJ002572 transcriptional unit N143 N143 AF051782 diaphanous homolog 1 (Drosophila) DIAPH1 AW973834 ESTs NM_004120 “guanylate binding protein 2, interferon- GBP2 inducible” D26054 “fructose-1,6-bisphosphatase 1” FBP1 BC004948 “Homo sapiens, clone MGC: 10846 IMAGE: 3616550, mRNA, complete cds” H71805 myeloid cell leukemia sequence 1 (BCL2- MCL1 related) NM_003033 “sialyltransferase 4A (beta-galactosidase SIAT4A alpha-2,3-sialytransferase)” NM_014361 contactin 5 CNTN5 AI631159 “solute carrier family 2 (facilitated glucose SLC2A3 transporter), member 3” NM_017617 hypothetical protein FLJ20005 FLJ20005 BC003070 GATA binding protein 3 GATA3 AI971258 seven in absentia homolog 1 (Drosophila) SIAH1 NM_002908 v-rel reticuloendotheliosis viral oncogene REL homolog (avian) NM_014005 protocadherin alpha 9 PCDHA9 M81104 CD34 antigen CD34 NM_030804 hypothetical protein DKFZp434E2135 DKFZP434E2135 AL021977 v-maf musculoaponeurotic fibrosarcoma MAFF oncogene homolog F (avian) NM_006931 “solute carrier family 2 (facilitated glucose SLC2A3 transporter), member 3” M81635 erythrocyte membrane protein band 7.2 EPB72 (stomatin) BF516433 cylindromatosis (turban tumor syndrome) CYLD AK027071 transforming growth factor beta-stimulated TSC22 protein TSC-22 BE677761 hypothetical protein PRO1584 PRO1584 L07555 “CD69 antigen (p60, early T-cell activation CD69 antigen)” AA778684 “solute carrier family 2 (facilitated glucose SLC2A3 transporter), member 3” NM_024875 hypothetical protein FLJ12921 FLJ12921 NM_006502 “polymerase (DNA directed), eta” POLH NM_002600 “phosphodiesterase 4B, cAMP-specific PDE4B (phosphodiesterase E4 dunce homolog, Drosophila)” NM_002856 poliovirus receptor-related 2 (herpesvirus PVRL2 entry mediator B) BC005254 “C-type (calcium dependent, carbohydrate- CLECSF2 recognition domain) lectin, superfamily member 2 (activation-induced)” NM_005346 heat shock 70 kDa protein 1B HSPA1B BC000145 “H1 histone family, member 0” H1F0 NM_004938 death-associated protein kinase 1 DAPK1 L20966 “phosphodiesterase 4B, cAMP-specific PDE4B (phosphodiesterase E4 dunce homolog, Drosophila)” D86586 stem cell growth factor; lymphocyte secreted SCGF C-type lectin NM_014745 KIAA0233 gene product KIAA0233 NM_015136 stabilin 1 STAB1 NM_005896 “isocitrate dehydrogenase 1 (NADP+), IDH1 soluble” AW149405 neurexin 1 NRXN1 X72501 T cell receptor delta locus TRD NM_024530 hypothetical protein FLJ23306 FLJ23306 BC005127 adipose differentiation-related protein ADFP AF031824 cystatin F (leukocystatin) CST7 NM_002379 “matrilin 1, cartilage matrix protein” MATN1 NM_004049 BCL2-related protein A1 BCL2A1 NM_000713 biliverdin reductase B (flavin reductase BLVRB (NADPH)) NM_005767 purinergic receptor (family A group 5) P2Y5 AL512728 Homo sapiens mRNA; cDNA DKFZp547P082 (from clone DKFZp547P082) NM_000519 “hemoglobin, delta” HBD NM_002727 “proteoglycan 1, secretory granule” PRG1 X77737 “solute carrier family 4, anion exchanger, SLC4A1 member 1 (erythrocyte membrane protein band 3, Diego blood group)” AB035266 neurexin 2 NRXN2 AV720514 “ESTs, Weakly similar to hypothetical protein FLJ20489 [Homo sapiens] [H. sapiens]” AL562152 SH3-domain binding protein 5 (BTK- SH3BP5 associated) NM_024703 hypothetical protein FLJ22593 FLJ22593 J03223 “proteoglycan 1, secretory granule” PRG1 AF153330 “solute carrier family 19 (thiamine SLC19A2 transporter), member 2” NM_000591 CD14 antigen CD14 BG035761 suppressor of cytokine signaling 3 SSI-3 AB014511 “ATPase, Class II, type 9A” ATP9A AF130113

TABLE 7A Top genes discriminating vincristine resistant and sensitive B- lineage ALL: Genes down-regulated in vincristine resistant B-lineage ALL NCBI Gene R/S Accession Probe ID Gene Name Symbol ratio Number 200593_s_at heterogeneous nuclear HNRPU 0.76 BC003621 ribonucleoprotein U 202209_at LSM3 homolog, U6 LSM3 0.77 NM_014463 small nuclear RNA associated 217733_s_at thymosin, beta 10 TMSB10 0.78 NM_021103 200031_s_at ribosomal protein S11 RPS11 0.84 NM_001015 200088_x_at cDNA (AK026491) 0.79 AK026491 213377_x_at complement C1S 0.78 AI799007 component 1, s subcomponent 200781_s_at ribosomal protein RPS15A 0.81 NM_001019 S15a 200909_s_at ribosomal protein, RPLP2 0.85 NM_001004 large P2 218672_at hypothetical protein MGC3180 0.70 NM_024041 MGC3180 208690_s_at PDZ and LIM domain PDLIM1 0.53 BC000915 1 (elfin) 218608_at putative ATPase HSA9947 0.10 NM_022089 202598_at S100 calcium binding S100A13 0.69 NM_005979 protein A13 201268_at non-metastatic cells 2, NME2 0.67 NM_002512 protein (NM23B) expressed in 210240_s_at cyclin-dependent CDKN2D U20498 kinase inhibitor 2D 0.66 (p19, inhibits CDK4) 201426_s_at ribosomal protein, RPLP2 0.52 AI922599 large P2 217523_at CD44 antigen CD44 0.30 AV700298 204490_s_at CD44 antigen CD44 0.36 M24915

TABLE 7B Top genes discriminating vincristine resistant and sensitive B- lineage ALL: Genes up-regulated in vincristine resistant B-lineage ALL NCBI R/S Accession Probe ID Gene Name Gene Symbol ratio Number 218325_s_at death associated DATF1 1.59 NM_022105 transcription factor 1 207753_at zinc finger protein 304 ZNF304 1.66 NM_020657 201851_at SH3-domain GRB2- SH3GL1 1.52 NM_003025 like 1 210162_s_at nuclear factor of NFATC1 1.80 U08015 activated T-cells, cytoplasmic, calcineurin-depe 213831_at major HLA-DQA1 3.55 X00452 histocompatibility complex, class II, DQ alpha 1 215127_s_at RNA binding motif, RBMS1 1.38 AL517946 single stranded interacting protein 1 218647_s_at hypothetical protein FLJ23476 1.28 NM_024640 FLJ23476 204914_s_at ESTs, Weakly similar 17.68 AI360875 to F36H12.3.p 219528_s_at B-cell CLL/lymphoma BCL11B 2.11 NM_022898 11B (zinc finger protein) 213604_at Homo sapiens clone 1.25 AW451236 24582 mRNA sequence 212037_at pinin, desmosome PNN 1.49 Y09703 associated protein 202392_s_at phosphatidylserine PISD 1.43 NM_014338 decarboxylase 212492_s_at KIAA0876 protein KIAA0876 1.46 AW237172 209705_at ESTs 1.30 AF073293 204837_at myotubularin related MTMR9 1.40 AL080178 protein 9 212438_at putative nucleic acid RY1 1.57 BG252325 binding protein RY-1 200757_s_at calumenin CALU 1.28 NM_001219 202946_s_at BTB (POZ) domain BTBD3 1.79 NM_014962 containing 3 55872_at KIAA1196 protein KIAA1196 1.54 AI493119 218951_s_at hypothetical protein FLJ11323 1.69 NM_018390 FLJ11323 213939_s_at Homo sapiens cDNA 4.12 AI871641 FLJ12012 fis, clone HEMBB1001668. 212222_at proteasome activator PA200 1.40 D38521 200 kDa 206033_s_at desmocollin 3 DSC3 1.72 NM_001941 202668_at ephrin-B2 EFNB2 2.15 BF001670 218642_s_at hypothetical protein MGC2217 1.34 NM_024300 MGC2217 212345_s_at hypothetical protein DKFZP586F2423 1.78 BE675139 DKFZp586F2423 203910_at PTPL1-associated PARG1 2.42 NM_004815 RhoGAP 1 213301_x_at transcriptional TIF1 2.55 AL538264 intermediary factor 1 204391_x_at transcriptional TIF1 2.91 NM_015905 intermediary factor 1 204849_at transcription factor- TCFL5 5.26 NM_006602 like 5 (basic helix- loop-helix) 221011_s_at likely ortholog of LBH 1.36 NM_030915 mouse limb-bud and heart gene 213017_at abhydrolase domain ABHD3 2.69 AL534702 containing 3 206231_at potassium KCNN1 3.29 NM_002248 intermediate/small conductance calcium- activated ch 202517_at collapsin response CRMP1 2.59 NM_001313 mediator protein 1 209296_at protein phosphatase PPM1B 1.40 AF136972 1B (formerly 2C), magnesium-dependent 212956_at KIAA0882 protein KIAA0882 3.64 AB020689 219471_at chromosome 13 open C13orf18 2.31 NM_025113 reading frame 18 44790_s_at chromosome 13 open C13orf18 3.13 AI129310 reading frame 18 204434_at spermatogenesis SPATA2 1.36 NM_006038 associated 2 203707_at zinc finger protein 263 ZNF263 1.32 NM_005741 213225_at protein phosphatase PPM1B 1.45 AJ271832 1B (formerly 2C), magnesium-dependent 213360_s_at POM121 membrane POM121 1.32 AA514622 glycoprotein (rat)

TABLE 7C Genes discriminating vincristine resistant and sensitive B-lineage ALL to the 0.001 < p < 0.01 level by both T-test and Wilcoxon: Genes down- regulated in vincristine resistant B-lineage ALL NCBI Accession Number Gene Name Gene Symbol NM_022089 putative ATPase HSA9947 NM_018465 uncharacterized hematopoietic stem/progenitor MDS030 cells protein MDS030 NM_016071 mitochondrial ribosomal protein S33 MRPS33 AV700298 “ESTs, Highly similar to CD44_HUMAN CD44 antigen precursor (Phagocytic glycoprotein I) (PGP-1) (HUTCH-I) (Extracellular matrix receptor-III) (ECMR-III) (GP90 lymphocyte homing/adhesion receptor) (Hermes antigen) (Hyaluronate receptor) (Heparan sulfate pro AB028839 “ubiquitination factor E4B (UFD2 homolog, UBE4B yeast)” NM_002452 nudix (nucleoside diphosphate linked moiety X)-type NUDT1 motif 1 BF513430 DKFZP586J0619 protein DKFZP586J0619 BC002906 uridine monophosphate kinase UMPK Z00008 NM_003645 “solute carrier family 27 (fatty acid transporter), SLC27A2 member 2” BG340670 immunoglobulin heavy constant mu IGHM M24915 CD44 antigen (homing function and Indian blood CD44 group system) AV764378 “RNA, U2 small nuclear” RNU2 BC004372 CD44 antigen (homing function and Indian blood CD44 group system) AI493245 CD44 antigen (homing function and Indian blood CD44 group system) NM_002339 lymphocyte-specific protein 1 LSP1 NM_001553 insulin-like growth factor binding protein 7 IGFBP7 NM_017518 three prime repair exonuclease 2 TREX2 NM_002961 “S100 calcium binding protein A4 (calcium S100A4 protein, calvasculin, metastasin, murine placental homolog)” NM_002765 phosphoribosyl pyrophosphate synthetase 2 PRPS2 AF098641 “Homo sapiens CD44 isoform RC (CD44) mRNA, complete cds” NM_004385 chondroitin sulfate proteoglycan 2 (versican) CSPG2 NM_004039 annexin A2 ANXA2 NM_003537 “H3 histone family, member L” H3FL NM_000610 CD44 antigen (homing function and Indian blood CD44 group system) BC003068 “solute carrier family 19 (folate transporter), SLC19A1 member 1” AF199015 villin 2 (ezrin) VIL2 BE903880 CD44 antigen (homing function and Indian blood CD44 group system) NM_004284 chromodomain helicase DNA binding protein 1- CHD1L like BE908217 annexin A2 ANXA2 AA476303 immunoglobulin kappa constant IGKC L38969 thrombospondin 3 THBS3 NM_001819 chromogranin B (secretogranin 1) CHGB NM_006907 pyrroline-5-carboxylate reductase 1 PYCR1 BC001388 annexin A2 ANXA2 NM_002712 “protein phosphatase 1, regulatory subunit 7” PPP1R7 NM_021827 hypothetical protein FLJ23514 FLJ23514 BC000915 PDZ and LIM domain 1 (elfin) PDLIM1 BC000988 hypothetical protein MGC5457 MGC5457 NM_000626 CD79B antigen (immunoglobulin-associated beta) CD79B M28882 melanoma cell adhesion molecule MCAM NM_000884 IMP (inosine monophosphate) dehydrogenase 2 IMPDH2 AI832239 mitochondrial ribosomal protein L23 MRPL23 AL525086 UDP-N-acetyl-alpha-D- GALNT2 galactosamine:polypeptide N- acetylgalactosaminyltransferase 2 (GalNAc-T2) AI922599 vimentin VIM AA112507 U6 snRNA-associated Sm-like protein LSM4 AI688812 RAS guanyl releasing protein 2 (calcium and RASGRP2 DAG-regulated) U13699 “caspase 1, apoptosis-related cysteine protease CASP1 (interleukin 1, beta, convertase)” BC004291 hypothetical protein MGC17226 MGC17226 L04636 “complement component 1, q subcomponent C1QBP binding protein” NM_001428 “enolase 1, (alpha)” ENO1 AV748469 SEC14-like 1 (S. cerevisiae) SEC14L1 NM_014257 CD209 antigen-like CD209L NM_030796 hypothetical protein DKFZp564K0822 DKFZP564K0822 AV655640 “CCAAT/enhancer binding protein (C/EBP), CEBPD delta” NM_004089 “delta sleep inducing peptide, immunoreactor” DSIPI AF089868 melanoma cell adhesion molecule MCAM NM_003931 “WAS protein family, member 1” WASF1 U20498 “cyclin-dependent kinase inhibitor 2D (p19, CDKN2D inhibits CDK4)” NM_003916 “adaptor-related protein complex 1, sigma 2 AP1S2 subunit” NM_005979 S100 calcium binding protein A13 S100A13 NM_006817 chromosome 12 open reading frame 8 C12orf8 NM_024041 hypothetical protein MGC3180 MGC3180 AF061735 “ATP synthase, H+ transporting, mitochondrial ATP5H F0 complex, subunit d” BE891920 “actin related protein 2/3 complex, subunit 4, ARPC4 20 kDa” J04423 BG395660 “ubiquitin-conjugating enzyme E2G 2 (UBC7 UBE2G2 homolog, yeast)” NM_012458 translocase of inner mitochondrial membrane 13 TIMM13 homolog (yeast) NM_004078 cysteine and glycine-rich protein 1 CSRP1 NM_002512 “non-metastatic cells 2, protein (NM23B) NME2 expressed in” NM_004271 “MD-1, RP105-associated” MD-1 NM_005174 “ATP synthase, H+ transporting, mitochondrial ATP5C1 F1 complex, gamma polypeptide 1” AI669379 “Homo sapiens cDNA FLJ35429 fis, clone SMINT2002126” NM_006294 ubiquinol-cytochrome c reductase binding protein UQCRB J04423 J04423 NM_001697 “ATP synthase, H+ transporting, mitochondrial ATP5O F1 complex, O subunit (oligomycin sensitivity conferring protein)” NM_004374 cytochrome c oxidase subunit VIc COX6C AA406605 weakly similar to glutathione peroxidase 2 CL683 AF199015 villin 2 (ezrin) VIL2 NM_014463 Lsm3 protein LSM3 NM_003134 signal recognition particle 14 kDa (homologous SRP14 Alu RNA binding protein) J04423 M26700 ubiquinol-cytochrome c reductase binding protein UQCRB BE675435 core promoter element binding protein COPEB NM_002128 high-mobility group box 1 HMGB1 BC000931 “ATP synthase, H+ transporting, mitochondrial ATP5C1 F1 complex, gamma polypeptide 1” AV702405 emopamil binding protein (sterol isomerase) EBP BC003621 heterogeneous nuclear ribonucleoprotein U HNRPU (scaffold attachment factor A) AW451954 adaptor-associated kinase 1 AAK1 U13698 “caspase 1, apoptosis-related cysteine protease CASP1 (interleukin 1, beta, convertase)” AB035745 Down syndrome critical region gene 5 DSCR5 M29277 melanoma cell adhesion molecule MCAM NM_003611 oral-facial-digital syndrome 1 OFD1 AF116273 BCL2-associated athanogene BAG1 BF669264 “Human erbB3 binding protein EBP1 mRNA, complete cds” BE311760 high-mobility group box 1 HMGB1 NM_016199 U6 snRNA-associated Sm-like protein LSm7 LOC51690 AF116639 chromosome 14 open reading frame 2 C14orf2 NM_003756 “eukaryotic translation initiation factor 3, subunit EIF3S3 3 gamma, 40 kDa” AA555113 “ribosomal protein, large, P0” RPLP0 AL136179 SRY (sex determining region Y)-box 4 SOX4 AU151801 “complement component 1, q subcomponent C1QBP binding protein” AL110191 “delta sleep inducing peptide, immunoreactor” DSIPI NM_031286 SH3 domain binding glutamic acid-rich protein SH3BGRL3 like 3 BC001865 “ESTs, Highly similar to ribosomal protein S2; 40S ribosomal protein S2 [Homo sapiens] [H. sapiens]” AF348514 “prothymosin, alpha (gene sequence 28)” PTMA X03453 NM_021103 “thymosin, beta 10” TMSB10 BF125158 ribosomal protein S2 RPS2 AF257099 AK026491 ribosomal protein L12 RPL12 BC006483 ribosomal protein L3 RPL3 AL133228 AI799007 ribosomal protein S12 RPS12 NM_000967 ribosomal protein L3 RPL3 J04423 BC001360 “ras homolog gene family, member A” ARHA NM_000984 ribosomal protein L23a RPL23A BC000523 ribosomal protein S24 RPS24 L22453 U43701 ribosomal protein L23a RPL23A BC000514 ribosomal protein L13a RPL13A BC006337 “adaptor-related protein complex 2, sigma 1 AP2S1 subunit” AA838274 ribosomal protein L14 RPL14 AA630314 ribosomal protein S2 RPS2 J04423 NM_001025 ribosomal protein S23 RPS23 BE305165 “protein phosphatase 1, regulatory (inhibitor) PPP1R14B subunit 14B” NM_000973 ribosomal protein L8 RPL8 NM_001207 basic transcription factor 3 BTF3 NM_001003 “ribosomal protein, large, P1” RPLP1 NM_001403 cyclin D1 (PRAD1: parathyroid adenomatosis 1) CCND1 NM_000980 ribosomal protein L18a RPL18A NM_001019 ribosomal protein S15a RPS15A AA281332 ribosomal protein L12 RPL12 NM_001001 ribosomal protein L36a-like RPL36AL AW188940 beta-2-microglobulin B2M AB009010 ubiquitin C UBC NM_000976 ribosomal protein L12 RPL12 X74070 basic transcription factor 3 BTF3 NM_022551 ribosomal protein S18 RPS18 NM_001402 eukaryotic translation elongation factor 1 alpha 1 EEF1A1 NM_001007 “ribosomal protein S4, X-linked” RPS4X NM_000971 ribosomal protein L7 RPL7 NM_006013 ribosomal protein L10 RPL10 NM_000993 ribosomal protein L31 RPL31 NM_001015 ribosomal protein S11 RPS11 X03453 NM_012423 ribosomal protein L13a RPL13A NM_000990 ribosomal protein L27a RPL27A NM_001032 ribosomal protein S29 RPS29 L05095 hypothetical protein FLJ22875 FLJ22875 BC003655 “ribosomal protein, large, P0” RPLP0 NM_001017 ribosomal protein S13 RPS13 NM_000981 ribosomal protein L19 RPL19 NM_021029 ribosomal protein L36A RPL36A AI953822 “ribosomal protein, large, P0” RPLP0 AI734929 “poly(A) binding protein, cytoplasmic 1” PABPC1 NM_001004 “ribosomal protein, large P2” RPLP2 AI721229 hypothetical protein FLJ20030 FLJ20030 BE786672 eukaryotic translation elongation factor 1 alpha 1 EEF1A1 BC001675 ribosomal protein L13a RPL13A J04423 AI183766 ribosomal protein S2 RPS2 NM_001002 “ribosomal protein, large, P0” RPLP0 BF686442 “prothymosin, alpha (gene sequence 28)” PTMA BC001019 ribosomal protein L39 RPL39 AF116710 ribosomal protein S14 RPS14 BC000354 ribosomal protein S28 RPS28 AK026525 glyceraldehyde-3-phosphate dehydrogenase GAPD BF942308 ribosomal protein L13a RPL13A AF072098 NM_021104 ribosomal protein L41 RPL41 BE964125 eukaryotic translation elongation factor 1 alpha 1 EEF1A1

TABLE 7D Genes discriminating vincristine resistant and sensitive B-lineage ALL to the 0.001 < p < 0.01 level by both T-test and Wilcoxon: Genes up-regulated in vincristine resistant B-lineage ALL NCBI Accession Number Gene Name Gene Symbol NM_024116 hypothetical protein MGC5306 MGC5306 BF690062 polypyrimidine tract binding protein 1 PTBP1 X62006 polypyrimidine tract binding protein 1 PTBP1 NM_005626 “splicing factor, arginine/serine-rich 4” SFRS4 NM_003663 CGG triplet repeat binding protein 1 CGGBP1 NM_025160 hypothetical protein FLJ21016 FLJ21016 L35253 mitogen-activated protein kinase 14 MAPK14 AF072814 likely ortholog of mouse metal response element M96 binding transcription factor 2 NM_007375 TAR DNA binding protein TARDBP NM_005109 oxidative-stress responsive 1 OSR1 NM_016146 PTD009 protein PTD009 NM_005759 abl-interactor 2 ABI-2 AL041728 slingshot 1 SSH1 AI344075 gamma-glutamyltransferase 2 GGT2 AI769637 UDP-glucuronic acid/UDP-N- UGTREL7 acetylgalactosamine dual transporter NM_017706 hypothetical protein FLJ20195 FLJ20195 NM_000801 “FK506 binding protein 1A, 12 kDa” FKBP1A NM_002537 ornithine decarboxylase antizyme 2 OAZ2 NM_018282 paraspeckle protein 1 PSP1 AK024029 modulator of apoptosis 1 MAP-1 NM_023924 hypothetical protein FLJ13441 FLJ13441 NM_018146 putative RNA methyltransferase FLJ10581 AI133727 likely ortholog of rat zinc-finger antiviral protein ZAP AF104913 “eukaryotic translation initiation factor 4 gamma, 1” EIF4G1 AK023188 “protein phosphatase 1, regulatory (inhibitor) PPP1R13B subunit 13B” NM_012124 “cysteine and histidine-rich domain (CHORD)- CHORDC1 containing, zinc binding protein 1” NM_014517 upstream binding protein 1 (LBP-1a) UBP1 AL514076 sarcoma amplified sequence SAS NM_030955 “a disintegrin-like and metalloprotease ADAMTS12 (reprolysin type) with thrombospondin type 1 motif, 12” AV682285 RE1-silencing transcription factor REST NM_005428 vav 1 oncogene VAV1 NM_002130 3-hydroxy-3-methylglutaryl-Coenzyme A HMGCS1 synthase 1 (soluble) NM_017895 DEAD/H (Asp-Glu-Ala-Asp/His) box DDX27 polypeptide 27 NM_004738 VAMP (vesicle-associated membrane protein)- VAPB associated protein B and C AW299555 “ubiquitin-conjugating enzyme E2G 1 (UBC7 UBE2G1 homolog, C. elegans)” AA156948 PRP4 pre-mRNA processing factor 4 homolog B PRPF4B (yeast) NM_017892 formin binding protein 3 FNBP3 NM_002266 “karyopherin alpha 2 (RAG cohort 1, importin KPNA2 alpha 1)” AL096828 chromosome 20 open reading frame 21 C20orf21 AA514622 KIAA0618 gene product KIAA0618 AL120741 apyrase SHAPY NM_018032 LUC7-like (S. cerevisiae) LUC7L AI638771 “phosphate cytidylyltransferase 1, choline, alpha PCYT1A isoform” U17714 suppression of tumorigenicity 13 (colon ST13 carcinoma) (Hsp70 interacting protein) AF254083 zinc finger protein 278 ZNF278 AW664421 suppressor of cytokine signaling 5 SOCS5 AW451236 Homo sapiens clone 24582 mRNA sequence NM_015626 SOCS box-containing WD protein SWiP-1 WSB1 NM_024640 hypothetical protein FLJ23476 FLJ23476 BC002557 hypothetical protein MGC2306 MGC2306 NM_002131 high mobility group AT-hook 1 HMGA1 NM_005044 “protein kinase, X-linked” PRKX NM_014247 PDZ domain containing guanine nucleotide PDZ-GEF1 exchange factor(GEF)1 AL136598 protein associated with PRK1 AWP1 AL110238 DKFZP566E104 protein DKFZP566E104 BC005247 isopentenyl-diphosphate delta isomerase IDI1 NM_014577 bromodomain containing 1 BRD1 AI744148 KIAA0431 protein KIAA0431 NM_006999 polymerase (DNA directed) sigma POLS NM_002657 pleiomorphic adenoma gene-like 2 PLAGL2 NM_018182 hypothetical protein FLJ10700 FLJ10700 NM_017896 chromosome 20 open reading frame 11 C20orf11 NM_012406 PR domain containing 4 PRDM4 BG033764 likely ortholog of mouse metal response element M96 binding transcription factor 2 AI525402 hypothetical protein FLJ11939 FLJ11939 AI123320 “eukaryotic translation initiation factor 3, subunit EIF3S10 10 theta, 150/170 kDa” BC001686 “methionine adenosyltransferase II, alpha” MAT2A AI937543 DC12 protein DC12 AL136896 suppressor of cytokine signaling 5 SOCS5 NM_001219 calumenin CALU AL050318 TGFB-induced factor 2 (TALE family TGIF2 homeobox) N48361 Homo sapiens mRNA; cDNA DKFZp564O1016 (from clone DKFZp564O1016) NM_003430 “zinc finger protein 91 (HPF7, HTF10)” ZNF91 X76302 putative nucleic acid binding protein RY-1 RY1 AL571424 NS1-associated protein 1 NSAP1 NM_005741 zinc finger protein 263 ZNF263 NM_021031 BC005147 “FK506 binding protein 1A, 12 kDa” FKBP1A NM_001046 “solute carrier family 12 SLC12A2 (sodium/potassium/chloride transporters), member 2” AW003091 “Homo sapiens cDNA FLJ38849 fis, clone MESAN2008936” NM_002056 glutamine-fructose-6-phosphate transaminase 1 GFPT1 NM_015959 CGI-31 protein LOC51075 NM_015973 galanin-related peptide LOC51083 BG292233 insulin induced gene 1 INSIG1 BC004191 dynactin 4 MGC3248 Z97056 Homo sapiens mRNA; cDNA DKFZp586K2322 (from clone DKFZp586K2322) NM_003330 thioredoxin reductase 1 TXNRD1 NM_022118 cutaneous T-cell lymphoma tumor antigen se70-2 SE70-2 AF254088 zinc finger protein 278 ZNF278 NM_004368 calponin 2 CNN2 NM_016598 “zinc finger, DHHC domain containing 3” ZDHHC3 D89053 “fatty-acid-Coenzyme A ligase, long-chain 3” FACL3 AA156865 Homo sapiens mRNA; cDNA DKFZp564O0122 (from clone DKFZp564O0122) NM_006526 zinc finger protein 217 ZNF217 NM_030825 AF073310 insulin receptor substrate 2 IRS2 AI141670 hypothetical protein MGC21688 MGC21688 AK022555 KIAA0618 gene product KIAA0618 NM_024300 hypothetical protein MGC2217 MGC2217 NM_013316 “CCR4-NOT transcription complex, subunit 4” CNOT4 NM_030915 likely ortholog of mouse limb-bud and heart gene LBH BC000927 poly(A) polymerase alpha PAPOLA BE963245 F-box and WD-40 domain protein 1B FBXW1B AU145005 Sp3 transcription factor SP3 NM_015339 activity-dependent neuroprotector ADNP BG536224 immunoglobulin kappa constant IGKC NM_007358 likely ortholog of mouse metal response element M96 binding transcription factor 2 NM_020119 likely ortholog of rat zinc-finger antiviral protein ZAP AB014593 synovial sarcoma translocation gene on SS18L1 chromosome 18-like 1 AI806207 SNF-1 related kinase SNRK NM_018043 hypothetical protein FLJ10261 FLJ10261 AF136972 “protein phosphatase 1B (formerly 2C), PPM1B magnesium-dependent, beta isoform” BF590997 hypothetical protein FLJ10707 FLJ10707 NM_006038 spermatogenesis associated 2 SPATA2 AL517946 “RNA binding motif, single stranded interacting RBMS1 protein 1” NM_002647 “phosphoinositide-3-kinase, class 3” PIK3C3 D26069 “centaurin, beta 2” CENTB2 NM_016265 GIOT-3 for gonadotropin inducible transcription GIOT-3 repressor-3 NM_031214 hypothetical protein AF311304 AF311304 NM_025078 hypothetical protein FLJ22378 FLJ22378 NM_003031 seven in absentia homolog 1 (Drosophila) SIAH1 NM_014011 suppressor of cytokine signaling 5 SOCS5 NM_014887 hypothetical protein from BCRA2 region CG005 AL080178 myotubularin related protein 9 MTMR9 D50911 KIAA0121 gene product KIAA0121 AW470003 KIAA0143 protein KIAA0143 AF009267 Homo sapiens clone FBA1 Cri-du-chat region mRNA NM_019034 “ras homolog gene family, member F (in ARHF filopodia)” BE256900 KIAA0876 protein KIAA0876 NM_018616 hypothetical protein PRO2037 PRO2037 N22859 KIAA0934 protein KIAA0934 AB002344 KIAA0346 protein KIAA0346 X72631 “nuclear receptor subfamily 1, group D, member NR1D1 1” NM_019591 zinc finger protein 26 (KOX 20) ZNF26 AU143855 proteasome activator 200 kDa PA200 AI333651 frizzled homolog 7 (Drosophila) FZD7 AA129753 “Rab geranylgeranyltransferase, beta subunit” RABGGTB NM_014338 phosphatidylserine decarboxylase PISD AW237172 KIAA0876 protein KIAA0876 AJ297710 cell division cycle 2-like 5 (cholinesterase-related CDC2L5 cell division controller) AJ271832 “protein phosphatase 1B (formerly 2C), PPM1B magnesium-dependent, beta isoform” BF222893 protocadherin 16 dachsous-like (Drosophila) PCDH16 AA830884 fragile X mental retardation 1 FMR1 AW592227 “KH domain containing, RNA binding, signal KHDRBS1 transduction associated 1” BF969986 hypothetical protein FLJ38045 FLJ38045 AI823592 KIAA0423 protein KIAA0423 AB023227 KIAA1010 protein KIAA1010 BF508848 “pinin, desmosome associated protein” PNN NM_003025 SH3-domain GRB2-like 1 SH3GL1 NM_003928 CAAX box 1 CXX1 NM_018200 high-mobility group 20A HMG20A AA554945 “ESTs, Weakly similar to hypothetical protein FLJ20378 [Homo sapiens] [H. sapiens]” AW167793 glucosamine (N-acetyl)-6-sulfatase (Sanfilippo GNS disease IIID) NM_017792 hypothetical protein FLJ20373 FLJ20373 AF052128 immunoglobulin mu binding protein 2 IGHMBP2 NM_001241 cyclin T2 CCNT2 AK025298 autism-related protein 1 KIAA0442 NM_005180 hypothetical protein MGC12685 MGC12685 AI493119 KIAA1196 protein KIAA1196 AI829875 B-cell CLL/lymphoma 3 BCL3 NM_018274 AI700633 “Homo sapiens cDNA: FLJ22642 fis, clone HSI06970” NM_005187 “core-binding factor, runt domain, alpha subunit CBFA2T3 2; translocated to, 3” AW293531 N-myristoyltransferase 2 NMT2 NM_006235 “POU domain, class 2, associating factor 1” POU2AF1 BG252325 putative nucleic acid binding protein RY-1 RY1 NM_002162 intercellular adhesion molecule 3 ICAM3 BC000277 KIAA0712 gene product KIAA0712 BE256900 KIAA0876 protein KIAA0876 NM_017610 likely ortholog of mouse Arkadia DKFZp761D081 AF186779 RalGDS-like gene RGL AF055024 ankyrin repeat and SOCS box-containing 1 ASB1 AA485908 insulin receptor INSR NM_016839 “RNA binding motif, single stranded interacting RBMS1 protein 1” NM_012068 activating transcription factor 5 ATF5 NM_018114 hypothetical protein FLJ10496 FLJ10496 NM_014426 sorting nexin 5 SNX5 BE042976 hypothetical protein MGC17330 MGC17330 NM_021255 pellino homolog 2 (Drosophila) PELI2 NM_018390 hypothetical protein FLJ11323 FLJ11323 AK001821 MGC4170 protein MGC4170 BF439316 transmembrane protein with EGF-like and two TMEFF1 follistatin-like domains 1 AF070647 Homo sapiens clone 24438 mRNA sequence NM_022105 death associated transcription factor 1 DATF1 AW204564 HCF-binding transcription factor Zhangfei ZF NM_003194 TATA box binding protein TBP NM_005542 insulin induced gene 1 INSIG1 AL540260 hypothetical protein MGC17330 MGC17330 M60485 “fibroblast growth factor receptor 1 (fms-related FGFR1 tyrosine kinase 2, Pfeiffer syndrome)” AW270932 hypothetical protein FLJ20275 FLJ20275 NM_020408 CGI-203 protein CGI-203 BE675139 hypothetical protein DKFZp586F2423 DKFZP586F2423 AF082283 B-cell CLL/lymphoma 10 BCL10 U90304 iroquois homeobox protein 5 IRX5 U79283 D site of albumin promoter (albumin D-box) DBP binding protein NM_018383 hypothetical protein FLJ11294 FLJ11294 NM_005766 “FERM, RhoGEF (ARHGEF) and pleckstrin FARP1 domain protein 1 (chondrocyte-derived)” NM_001065 “tumor necrosis factor receptor superfamily, TNFRSF1A member 1A” NM_005981 sarcoma amplified sequence SAS AU147889 “Homo sapiens cDNA FLJ14122 fis, clone MAMMA1002033” NM_020657 zinc finger protein 304 ZNF304 U08015 “nuclear factor of activated T-cells, cytoplasmic, NFATC1 calcineurin-dependent 1” NM_014962 BTB (POZ) domain containing 3 BTBD3 NM_004456 enhancer of zeste homolog 2 (Drosophila) EZH2 AK023816 “Homo sapiens cDNA FLJ13754 fis, clone PLACE3000362” AI567426 “transducin-like enhancer of split 3 (E(sp1) TLE3 homolog, Drosophila)” NM_003082 “small nuclear RNA activating complex, SNAPC1 polypeptide 1, 43 kDa” NM_005815 Kruppel-type zinc finger (C2H2) ZK1 NM_002222 “inositol 1,4,5-triphosphate receptor, type 1” ITPR1 AL046979 “Homo sapiens cDNA FLJ32766 fis, clone TESTI2001862” NM_002193 “inhibin, beta B (activin AB beta polypeptide)” INHBB NM_001941 desmocollin 3 DSC3 NM_003478 cullin 5 CUL5 NM_005433 v-yes-1 Yamaguchi sarcoma viral oncogene YES1 homolog 1 NM_000147 “fucosidase, alpha-L-1, tissue” FUCA1 AC004010 “Homo sapiens cDNA FLJ35792 fis, clone TESTI2005759” NM_005308 G protein-coupled receptor kinase 5 GPRK5 NM_004415 “desmoplakin (DPI, DPII)” DSP NM_024994 hypothetical protein FLJ12595 FLJ12595 BC003105 “protein tyrosine phosphatase type IVA, member PTP4A3 3” X96588 RYK receptor-like tyrosine kinase RYK NM_005652 telomeric repeat binding factor 2 TERF2 NM_016929 chloride intracellular channel 5 CLIC5 U63332 “Human super cysteine rich protein mRNA, partial cds” NM_005842 sprouty homolog 2 (Drosophila) SPRY2 BF001670 ephrin-B2 EFNB2 NM_003507 frizzled homolog 7 (Drosophila) FZD7 AF153820 “potassium inwardly-rectifying channel, KCNJ2 subfamily J, member 2” NM_007079 “protein tyrosine phosphatase type IVA, member PTP4A3 3” NM_025113 hypothetical protein FLJ21562 FLJ21562 H49382 “ESTs, Weakly similar to hypothetical protein FLJ20378 [Homo sapiens] [H. sapiens]” AF021834 tissue factor pathway inhibitor (lipoprotein- TFPI associated coagulation inhibitor) BF031829 “Homo sapiens, clone IMAGE: 4242700, mRNA” NM_022898 B-cell CLL/lymphoma 11B (zinc finger protein) BCL11B AB020717 synaptojanin 1 SYNJ1 NM_005433 v-yes-1 Yamaguchi sarcoma viral oncogene YES1 homolog 1 AL538264 transcriptional intermediary factor 1 TIF1 AK026161 apyrase SHAPY NM_012447 stromal antigen 3 STAG3 NM_001313 collapsin response mediator protein 1 CRMP1 H16758 erythropoietin receptor EPOR NM_004815 PTPL1-associated RhoGAP 1 PARG1 NM_004049 BCL2-related protein A1 BCL2A1 NM_015905 transcriptional intermediary factor 1 TIF1 AB006624 KIAA0286 protein KIAA0286 AL534702 abhydrolase domain containing 3 ABHD3 NM_006822 “RAB40B, member RAS oncogene family” RAB40B M60459 erythropoietin receptor EPOR M16276 “major histocompatibility complex, class II, DQ HLA-DQB1 beta 1” AI129310 hypothetical protein FLJ21562 FLJ21562 NM_022161 baculoviral IAP repeat-containing 7 (livin) BIRC7 NM_002248 “potassium intermediate/small conductance KCNN1 calcium-activated channel, subfamily N, member 1” U42349 Putative prostate cancer tumor suppressor N33 AB020683 KIAA0876 protein KIAA0876 X00452 “major histocompatibility complex, class II, DQ HLA-DQA1 alpha 1” NM_016588 neuritin 1 NRN1 AV753028 transducin (beta)-like 1X-linked TBL1X AI348094 KIAA0882 protein KIAA0882 AL049313 Homo sapiens mRNA; cDNA DKFZp564B076 (from clone DKFZp564B076) L20433 “POU domain, class 4, transcription factor 1” POU4F1 NM_018159 nudix (nucleoside diphosphate linked moiety X)- NUDT11 type motif 11 AI884858 Putative prostate cancer tumor suppressor N33 AB028641 SRY (sex determining region Y)-box 11 SOX11 NM_006602 transcription factor-like 5 (basic helix-loop-helix) TCFL5 AI360875 SRY (sex determining region Y)-box 11 SOX11 AI040163 “calcium channel, voltage-dependent, beta 2 CACNB2 subunit” AI871641 KIAA0871 protein KIAA0871 NM_002307 “lectin, galactoside-binding, soluble, 7 (galectin LGALS7 7)” AL161995 neurturin NRTN AW157202 SRY (sex determining region Y)-box 11 SOX11

TABLE 8A Top genes discriminating L-asparaginase resistant and sensitive B-lineage ALL: Genes down-regulated in L-asparaginase resistant B-lineage ALL R/S NCBI Accession Probe ID Gene Name Gene Symbol ratio Number 208579_x_at histone 1, H2bk HIST1H2BK 0.49 NM_017445 209806_at histone 1, H2bk HIST1H2BK 0.6 BC000893 203521_s_at endocrine regulator ZFP318 0.54 NM_014345 212070_at G protein-coupled GPR56 0.39 AL554008 receptor 56 201015_s_at junction plakoglobin JUP 0.63 NM_021991 203388_at arrestin, beta 2 ARRB2 0.57 NM_004313 221760_at mannosidase, alpha, MAN1A1 0.39 BG287153 class 1A, member 1 221773_at Homo sapiens cDNA: HRC08686. 0.35 AW575374 FLJ22425 fis, clone 211559_s_at cyclin G2 CCNG2 0.63 L49506 218333_at CGI-101 protein F-LAN-1 0.71 NM_016041 218669_at hypothetical protein LOC57826 0.64 NM_021183 similar to small G proteins, especially RAP- 203311_s_at ADP-ribosylation factor 6 ARF6 0.67 M57763 203274_at coagulation factor VIII- F8A 0.62 NM_012151 associated (intronic transcript) 212643_at chromosome 14 open C14orf32 0.74 AI671747 reading frame 32 217750_s_at hypothetical protein FLJ13855 0.69 NM_023079 FLJ13855 201156_s_at RAB5C, member RAS RAB5C 0.71 AF141304 oncogene family 201140_s_at RAB5C, member RAS RAB5C 0.63 NM_004583 oncogene family

TABLE 8B Top genes discriminating L-asparaginase resistant and sensitive B-lineage ALL: Genes up-regulated in L-asparaginase resistant B-lineage ALL R/S NCBI Accession Probe ID Gene Name Gene Symbol ratio Number 220306_at hypothetical protein FLJ20202 1.87 NM_017709 FLJ20202 205131_x_at stem cell growth factor; SCGF 3.38 NM_002975 lymphocyte secreted C- type lectin 211709_s_at stem cell growth factor; SCGF 2.81 BC005810 lymphocyte secreted C- type lectin 201163_s_at insulin-like growth IGFBP7 2.02 NM_001553 factor binding protein 7 212886_at DKFZP434C171 protein DKFZP434C171 2.18 AL080169 202315_s_at breakpoint cluster BCR 1.57 NM_004327 region 211940_x_at H3 histone, family 3A H3F3A 1.22 BE869922 208755_x_at H3 histone, family 3A H3F3A 1.27 BF312331 213828_x_at H3 histone, family 3A H3F3A 1.27 AA477655 209602_s_at GATA binding protein 3 GATA3 6.54 AI796169 209604_s_at GATA binding protein 3 GATA3 3.12 BC003070 212481_s_at tropomyosin 4 TPM4 1.47 AI214061 217807_s_at glioma tumor suppressor GLTSCR2 1.43 NM_015710 candidate region gene 2 200005_at eukaryotic translation EIF3S7 1.39 NM_003753 initiation factor 3, subunit 7 zeta 217719_at eukaryotic translation EIF3S6IP 1.38 NM_016091 initiation factor 3, subunit 6 interacting pro 210501_x_at large tumor suppressor, 1.32 AF119846 Drosophilahomolog 1 211623_s_at fibrillarin FBL 1.5 M30448 200024_at ribosomal protein S5 RPS5 1.46 NM_001009 200651_at guanine nucleotide GNB2L1 1.27 NM_006098 binding protein (G protein) 200010_at ribosomal protein L11 RPL11 1.25 NM_000975 213080_x_at ribosomal protein L5 RPL5 1.37 BF214492 200034_s_at ribosomal protein L6 RPL6 1.35 NM_000970 200715_x_at ribosomal protein L13a RPL13A 1.42 BC000514 200689_x_at eukaryotic translation EEF1G 1.27 NM_001404 elongation factor 1 gamma 208692_at ribosomal protein S3 RPS3 1.25 U14990 211927_x_at similar to S22655 1.23 BE963164 translation elongation factor eEF-1 gamma chain 200089_s_at ribosomal protein L4 RPL4 1.3 AI953886 200705_s_at eukaryotic translation EEF1B2 1.46 NM_001959 elongation factor 1 beta 2 215963_x_at similar to S34195 1.39 Z98200 ribosomal protein L3, cytosolic 201217_x_at ribosomal protein L3 RPL3 1.42 NM_000967 211666_x_at ribosomal protein L3 RPL3 1.43 L22453 211073_x_at ribosomal protein L3 RPL3 1.43 BC006483 212039_x_at ribosomal protein L3 RPL3 1.38 BG339228 214167_s_at ribosomal protein, large, RPLP0 1.51 AA555113 P0 217740_x_at ribosomal protein L7a RPL7A 1.32 NM_000972 201818_at hypothetical protein FLJ12443 1.85 NM_024830 FLJ12443 215115_x_at neurotrophic tyrosine NTRK3 1.39 AI613045 kinase, receptor, type 3

TABLE 8C Genes discriminating L-asparaginase resistant and sensitive B-lineage ALL to the 0.001 < p < 0.01 level by both T-test and Wilcoxon: Genes down-regulated in L-asparaginase resistant B-lineage ALL NCBI Accession Number Gene Name Gene Symbol NM_003919 “sarcoglycan, epsilon” SGCE NM_002356 myristoylated alanine-rich protein kinase C MARCKS substrate AI348094 KIAA0882 protein KIAA0882 AL582836 paternally expressed 10 PEG10 AI983115 class I cytokine receptor WSX1 M68956 myristoylated alanine-rich protein kinase C MARCKS substrate NM_004443 EphB3 EPHB3 NM_005682 G protein-coupled receptor 56 GPR56 M37780 platelet/endothelial cell adhesion molecule PECAM1 (CD31 antigen) NM_001154 annexin A5 ANXA5 AW469573 mitogen inducible 2 MIG2 L20433 “POU domain, class 4, transcription factor 1” POU4F1 NM_002507 “nerve growth factor receptor (TNFR NGFR superfamily, member 16)” AI814527 a disintegrin and metalloproteinase domain 8 ADAM8 D55696 legumain LGMN AW134608 immunoglobulin heavy constant gamma 3 IGHG3 (G3m marker) NM_014879 G protein-coupled receptor 105 GPR105 AI718937 hypothetical protein BC013764 LOC115207 U76376 “harakiri, BCL2 interacting protein HRK (contains only BH3 domain)” AF220509 “TAF9-like RNA polymerase II, TATA box TAF9L binding protein (TBP)-associated factor, 31 kDa” BG287153 “mannosidase, alpha, class 1A, member 1” MAN1A1 AW575374 “ELK3, ETS-domain protein (SRF ELK3 accessory protein 2)” NM_004429 ephrin-B1 EFNB1 AF241787 Mitochondrial Acyl-CoA Thioesterase MT-ACT48 AI817041 G protein-coupled receptor RDC1 AL554008 G protein-coupled receptor 56 GPR56 AI970898 “Homo sapiens, clone IMAGE: 3833472, mRNA” NM_002736 “protein kinase, cAMP-dependent, PRKAR2B regulatory, type II, beta” AF176039 high mobility group AT-hook 1 HMGA1 AA551075 hypothetical protein BC013764 LOC115207 AB035482 basement membrane-induced gene ICB-1 NM_001552 insulin-like growth factor binding protein 4 IGFBP4 NM_006602 transcription factor-like 5 (basic helix-loop- TCFL5 helix) AB020681 KIAA0874 protein KIAA0874 NM_006237 “POU domain, class 4, transcription factor 1” POU4F1 NM_001629 arachidonate 5-lipoxygenase-activating ALOX5AP protein AK021738 expressed in activated T/LAK lymphocytes LAK-4P NM_002201 interferon stimulated gene 20 kDa ISG20 NM_014345 endocrine regulator HRIHFB2436 M15330 “interleukin 1, beta” IL1B AI655015 Homo sapiens mRNA; cDNA DKFZp586F2224 (from clone DKFZp586F2224) NM_002452 nudix (nucleoside diphosphate linked NUDT1 moiety X)-type motif 1 NM_001124 adrenomedullin ADM AA149594 TGFB inducible early growth response 2 TIEG2 U82277 “leukocyte immunoglobulin-like receptor, LILRA2 subfamily A (with TM domain), member 2” NM_000905 neuropeptide Y NPY NM_016229 cytochrome b5 reductase b5R.2 LOC51700 AW163148 myristoylated alanine-rich protein kinase C MARCKS substrate NM_001449 four and a half LIM domains 1 FHL1 NM_005652 telomeric repeat binding factor 2 TERF2 AF063002 four and a half LIM domains 1 FHL1 AI801013 holocytochrome c synthase (cytochrome c HCCS heme-lyase) BC000229 hypothetical protein MGC2488 MGC2488 AF220153 four and a half LIM domains 1 FHL1 NM_005815 Kruppel-type zinc finger (C2H2) ZK1 AF186779 RalGDS-like gene RGL AB001733 immunoglobulin lambda joining 3 IGLJ3 NM_017445 “H2B histone family, member S” H2BFS NM_019045 similar to rab11-binding protein FLJ11116 NM_004848 basement membrane-induced gene ICB-1 AF098518 four and a half LIM domains 1 FHL1 NM_005907 “mannosidase, alpha, class 1A, member 1” MAN1A1 BC005127 adipose differentiation-related protein ADFP NM_016256 N-acetylglucosamine-1-phosphodiester LOC51172 alpha-N-acetylglucosaminidase AJ251844 NM_006932 smoothelin SMTN NM_003644 growth arrest-specific 7 GAS7 NM_002408 “mannosyl (alpha-1,6-)-glycoprotein beta- MGAT2 1,2-N-acetylglucosaminyltransferase” AI718418 “stress 70 protein chaperone, microsome- STCH associated, 60 kDa” NM_004233 “CD83 antigen (activated B lymphocytes, CD83 immunoglobulin superfamily)” AV721430 “transcription factor 7-like 2 (T-cell TCF7L2 specific, HMG-box)” M85256 AI073984 interferon consensus sequence binding ICSBP1 protein 1 NM_000594 “tumor necrosis factor (TNF superfamily, TNF member 2)” BF970829 oxysterol binding protein-like 8 OSBPL8 NM_019597 heterogeneous nuclear ribonucleoprotein H2 (H′) HNRPH2 NM_006948 “stress 70 protein chaperone, microsome- STCH associated, 60 kDa” NM_004313 “arrestin, beta 2” ARRB2 BF732638 likely ortholog of mouse variant CSTF2T polyadenylation protein CSTF-64 AI659005 “ESTs, Moderately similar to unnamed protein product [Homo sapiens] [H. sapiens]” NM_003806 “harakiri, BCL2 interacting protein HRK (contains only BH3 domain)” NM_024576 hypothetical protein FLJ21079 FLJ21079 NM_014885 anaphase-promoting complex subunit 10 APC10 NM_018422 hypothetical protein DKFZp761K1423 DKFZp761K1423 AL050164 “chromodomain protein, Y chromosome- CDYL like” NM_006965 zinc finger protein 24 (KOX 17) ZNF24 NM_019034 “ras homolog gene family, member F (in ARHF filopodia)” NM_014061 APR-1 protein MAGEH1 AL523275 “Homo sapiens calmodulin-I (CALM1) mRNA, 3′UTR, partial sequence” U30894 N-sulfoglucosamine sulfohydrolase SGSH (sulfamidase) NM_000576 “interleukin 1, beta” IL1B NM_006359 “solute carrier family 9 (sodium/hydrogen SLC9A6 exchanger), isoform 6” L78132 “lectin, galactoside-binding, soluble, 8 LGALS8 (galectin 8)” AL542571 GrpE-like protein cochaperone HMGE BC004908 hypothetical protein MGC4655 MGC4655 AB011152 “centaurin, delta 1” CENTD1 L49506 cyclin G2 CCNG2 NM_017918 hypothetical protein FLJ20647 FLJ20647 NM_005230 “ELK3, ETS-domain protein (SRF ELK3 accessory protein 2)” NM_001774 CD37 antigen CD37 AA775177 “protein tyrosine phosphatase, receptor type, PTPRE E” AI191118 “ESTs, Moderately similar to cytokine receptor-like factor 2; cytokine receptor CRL2 precusor [Homo sapiens] [H. sapiens]” NM_004583 “RAB5C, member RAS oncogene family” RAB5C NM_002406 “mannosyl (alpha-1,3-)-glycoprotein beta- MGAT1 1,2-N-acetylglucosaminyltransferase” NM_000177 “gelsolin (amyloidosis, Finnish type)” GSN NM_000788 deoxycytidine kinase DCK NM_002448 msh homeo box homolog 1 (Drosophila) MSX1 NM_005842 sprouty homolog 2 (Drosophila) SPRY2 NM_018466 uncharacterized hematopoietic MDS031 stem/progenitor cells protein MDS031 NM_000698 arachidonate 5-lipoxygenase ALOX5 NM_021183 “hypothetical protein similar to small G LOC57826 proteins, especially RAP-2A” AI742626 HIV-1 Rev binding protein HRB NM_012151 coagulation factor VIII-associated (intronic F8A transcript) NM_003864 “sin3-associated polypeptide, 30 kDa” SAP30 BC000893 histone family member H2B/S BF432873 “proteasome (prosome, macropain) 26S PSMD11 subunit, non-ATPase, 11” NM_003088 “singed-like (fascin homolog, sea urchin) SNL (Drosophila)” NM_002835 “protein tyrosine phosphatase, non-receptor PTPN12 type 12” NM_006804 START domain containing 3 STARD3 NM_003730 ribonuclease 6 precursor RNASE6PL M17955 “major histocompatibility complex, class II, HLA-DQB1 DQ beta 1” AI653730 “Homo sapiens calmodulin-I (CALM1) mRNA, 3′UTR, partial sequence” NM_024613 phafin 2 FLJ13187 AA702701 platelet/endothelial cell adhesion molecule PECAM1 (CD31 antigen) BG495771 “Homo sapiens cDNA FLJ11918 fis, clone HEMBB1000272” U88964 interferon stimulated gene 20 kDa ISG20 AV694732 cullin 4B CUL4B BC000373 amyloid beta (A4) precursor-like protein 2 APLP2 AL049923 oxysterol binding protein-like 8 OSBPL8 X75208 EphB3 EPHB3 NM_012447 stromal antigen 3 STAG3 NM_006821 peroxisomal long-chain acyl-coA ZAP128 thioesterase AJ276888 “Mdm2, transformed 3T3 cell double MDM2 minute 2, p53 binding protein (mouse)” NM_020408 CGI-203 protein CGI-203 AA758755 “proteasome (prosome, macropain) activator PSME3 subunit 3 (PA28 gamma; Ki)” NM_017773 hypothetical protein FLJ20340 FLJ20340 Z24459 NM_018169 hypothetical protein FLJ10652 FLJ10652 BF677486 “thymosin, beta, identified in neuroblastoma TMSNB cells” Z25433 NM_018037 hypothetical protein FLJ10244 FLJ10244 BG427393 amyloid beta (A4) precursor-like protein 2 APLP2 AI653730 “Homo sapiens calmodulin-I (CALM1) mRNA, 3′UTR, partial sequence” NM_021991 junction plakoglobin JUP U15555 “serine palmitoyltransferase, long chain SPTLC2 base subunit 2” NM_024644 hypothetical protein FLJ21802 FLJ21802 AF217963 “melanoma antigen, family D, 1” MAGED1 NM_003524 “H2B histone family, member J” H2BFJ NM_007106 ubiquitin-like 3 UBL3 NM_001642 amyloid beta (A4) precursor-like protein 2 APLP2 BC006390 “mannosyl (alpha-1,6-)-glycoprotein beta- MGAT2 1,2-N-acetylglucosaminyltransferase” NM_006936 SMT3 suppressor of mif two 3 homolog 1 SMT3H1 (yeast) NM_014043 DKFZP564O123 protein DKFZP564O123 NM_002814 “proteasome (prosome, macropain) 26S PSMD10 subunit, non-ATPase, 10” AL560017 prohibitin PHB NM_014175 mitochondrial ribosomal protein L15 MRPL15 NM_016185 hematological and neurological expressed 1 HN1 NM_004508 isopentenyl-diphosphate delta isomerase IDI1 AI608725 “intercellular adhesion molecule 1 (CD54), ICAM1 human rhinovirus receptor” NM_001186 “BTB and CNC homology 1, basic leucine BACH1 zipper transcription factor 1” NM_018094 G1 to S phase transition 2 GSPT2 Y13786 a disintegrin and metalloproteinase domain ADAM19 19 (meltrin beta) NM_003199 transcription factor 4 TCF4 NM_020633 V1R-like 1 V1RL1 NM_005496 SMC4 structural maintenance of SMC4L1 chromosomes 4-like 1 (yeast) U82276 “leukocyte immunoglobulin-like receptor, LILRA2 subfamily A (with TM domain), member 2” NM_006520 t-complex-associated-testis-expressed 1-like TCTE1L NM_002484 “nucleotide binding protein 1 (MinD NUBP1 homolog, E.coli)” AI591354 heterogeneous nuclear ribonucleoprotein F HNRPF M25269 “ELK1, member of ETS oncogene family” ELK1 BE858180 paternally expressed 10 PEG10 BG338532 SMT3 suppressor of mif two 3 homolog 1 SMT3H1 (yeast) NM_016041 CGI-101 protein F-LAN-1 NM_005359 “MAD, mothers against decapentaplegic MADH4 homolog 4 (Drosophila)” AI361850 arachidonate 5-lipoxygenase ALOX5 AF141304 “RAB5C, member RAS oncogene family” RAB5C BE549732 “ESTs, Weakly similar to replication initiation region protein (60 kD); zinc finger proten AP4 [Homo sapiens] [H. sapiens]” NM_023079 hypothetical protein FLJ13855 FLJ13855 AI084226 regulator of Fas-induced apoptosis TOSO AV713053 hypothetical protein FLJ14547 FLJ14547 NM_016608 ALEX1 protein ALEX1 BG111168 chromosome 6 open reading frame 9 C6orf9 Z21533 hematopoietically expressed homeobox HHEX BC005123 “serine palmitoyltransferase, long chain SPTLC2 base subunit 2” BC006454 growth arrest-specific 7 GAS7 AI356398 “zinc finger protein 36, C3H type-like 2” ZFP36L2 M57763 ADP-ribosylation factor 6 ARF6 NM_001470 “gamma-aminobutyric acid (GABA) B GABBR1 receptor, 1” NM_024121 family with sequence similarity 11 member B FAM11B AA676803 “Homo sapiens, clone IMAGE: 5243069, mRNA” AK026678 stromal antigen 2 STAG2 NM_004354 cyclin G2 CCNG2 BC000903 high-mobility group box 2 HMGB2 NM_006561 “CUG triplet repeat, RNA binding protein CUGBP2 2” N22468 “MADS box transcription enhancer factor 2, MEF2C polypeptide C (myocyte enhancer factor 2C)” AF132362 heterogeneous nuclear ribonucleoprotein H3 HNRPH3 (2H9) AI927067 “Homo sapiens cDNA FLJ11918 fis, clone HEMBB1000272” BG397856 “major histocompatibility complex, class II, HLA-DQA1 DQ alpha 1” NM_006570 Ras-related GTP-binding protein RAGA AF342815 “lectin, galactoside-binding, soluble, 8 LGALS8 (galectin 8)” AW134535 cyclin G2 CCNG2 NM_001968 eukaryotic translation initiation factor 4E EIF4E AI139569 SWAP-70 protein SWAP70 NM_021183 “hypothetical protein similar to small G LOC57826 proteins, especially RAP-2A” BC004421 nucleolar cysteine-rich protein HSA6591 BG252842 hypothetical protein FLJ12619 FLJ12619 NM_005697 secretory carrier membrane protein 2 SCAMP2 NM_006333 nuclear DNA-binding protein C1D NM_005574 LIM domain only 2 (rhombotin-like 1) LMO2 NM_001529 hematopoietically expressed homeobox HHEX NM_014210 ecotropic viral integration site 2A EVI2A NM_025205 endothelial-derived gene 1 EG1 NM_005342 high-mobility group box 3 HMGB3 AI984421 GrpE-like protein cochaperone HMGE NM_002118 “major histocompatibility complex, class II, HLA-DMB DM beta” AF064605 death effector domain containing DEDD NM_007267 expressed in activated T/LAK lymphocytes LAK-4P NM_005638 synaptobrevin-like 1 SYBL1 NM_002634 prohibitin PHB AI131008 thyroid hormone receptor interactor 3 TRIP3 AU118026 “Homo sapiens cDNA FLJ11918 fis, clone HEMBB1000272” AL110243 SOCS box-containing WD protein SWiP-1 WSB1 BF433429 “Homo sapiens cDNA FLJ11918 fis, clone HEMBB1000272” AF114012 “tumor necrosis factor (ligand) superfamily, TNFSF13 member 13” M32577 AA502643 “tyrosine 3-monooxygenase/tryptophan 5- YWHAE monooxygenase activation protein, epsilon polypeptide” BC005147 “FK506 binding protein 1A, 12 kDa” FKBP1A AK001899 APG5 autophagy 5-like (S. cerevisiae) APG5L NM_017936 hypothetical protein FLJ20707 FLJ20707 BG390445 ubiquitin specific protease 10 USP10 AW165960 “protein tyrosine phosphatase type IVA, PTP4A1 member 1” AV728658 KIAA0592 protein KIAA0592 NM_018648 “nucleolar protein family A, member 3 NOLA3 (H/ACA small nucleolar RNPs)” BC006456 hypothetical protein FLJ10824 FLJ10824 U32645 E74-like factor 4 (ets domain transcription ELF4 factor) AK026674 transcription factor 4 TCF4 NM_000100 cystatin B (stefin B) CSTB M90686 “HLA-G histocompatibility antigen, class I, HLA-G G” NM_017917 hypothetical protein FLJ20644 FLJ20644 NM_021242 hypothetical protein STRAIT11499 STRAIT11499 NM_003336 ubiquitin-conjugating enzyme E2A (RAD6 UBE2A homolog) M29335 BC005247 isopentenyl-diphosphate delta isomerase IDI1 X72631 “nuclear receptor subfamily 1, group D, NR1D1 member 1” BE962615 sorting nexin 3 SNX3 NM_024064 hypothetical protein MGC5363 MGC5363 AI096477 zinc finger protein 363 ZNF363 NM_006460 HMBA-inducible HIS1 NM_007373 soc-2 suppressor of clear homolog (C. elegans) SHOC2 NM_030915 likely ortholog of mouse limb-bud and heart LBH gene AK026913 WIRE protein WIRE BE465032 hypothetical protein FLJ12619 FLJ12619 NM_001654 v-raf murine sarcoma 3611 viral oncogene ARAF1 homolog 1 BC004130 nuclear domain 10 protein NDP52 AI936769 “FK506 binding protein 1A, 12 kDa” FKBP1A BF592782 “Homo sapiens cDNA FLJ11918 fis, clone HEMBB1000272” NM_018149 hypothetical protein FLJ10587 FLJ10587 AF254088 zinc finger protein 278 ZNF278 NM_003244 TGFB-induced factor (TALE family TGIF homeobox) AL035588 transcription factor EB TFEB AK001029 ubiquilin 2 UBQLN2 AK023289 hypothetical protein P15-2 P15-2 NM_004162 “RAB5A, member RAS oncogene family” RAB5A AI671747 likely ortholog of mouse MAPK-interacting MISS and spindle-stabilizing protein BC001002 hypothetical protein DKFZp434N0650 DKFZp434N0650 NM_017698 hypothetical protein FLJ22679 FLJ22679 NM_002106 “H2A histone family, member Z” H2AFZ D13988 GDP dissociation inhibitor 2 GDI2 NM_004124 “glia maturation factor, beta” GMFB AF001212 “proteasome (prosome, macropain) 26S PSMD11 subunit, non-ATPase, 11” W48843 sprouty homolog 4 (Drosophila) SPRY4 NM_003523 “H2B histone family, member H” H2BFH U94831 transmembrane 9 superfamily member 1 TM9SF1 AI671747 likely ortholog of mouse MAPK-interacting MISS and spindle-stabilizing protein AI984479 “Homo sapiens cDNA FLJ33067 fis, clone TRACH2000148, weakly similar to POLY(A) POLYMERASE (EC 2.7.7.19)” AV726646 SMT3 suppressor of mif two 3 homolog 2 SMT3H2 (yeast) NM_003131 serum response factor (c-fos serum response SRF element-binding transcription factor) NM_005736 “ARP1 actin-related protein 1 homolog A, ACTR1A centractin alpha (yeast)” NM_002494 “NADH dehydrogenase (ubiquinone) 1, NDUFC1 subcomplex unknown, 1, 6 kDa” Z25435 NM_003591 cullin 2 CUL2 NM_016129 COP9 constitutive photomorphogenic COPS4 homolog subunit 4 (Arabidopsis) NM_005428 vav 1 oncogene VAV1 NM_018950 “major histocompatibility complex, class I, HLA-F F” AI768845 synaptophysin-like protein SYPL NM_006432 “Niemann-Pick disease, type C2” NPC2 AF279372 “inositol 1,3,4-triphosphate 5/6 kinase” ITPK1 AW873564 “ESTs, Weakly similar to YHS1_YEAST HYPOTHETICAL 21.3 KD PROTEIN IN MSH1-EPT1 INTERGENIC REGION [S. cerevisiae]” NM_006255 “protein kinase C, eta” PRKCH NM_016079 CGI-149 protein LOC51652 NM_022107 chromosome 6 open reading frame 9 C6orf9 M60334 “major histocompatibility complex, class II, HLA-DRA DR alpha” NM_002664 pleckstrin PLEK AW139179 fem-1 homolog b (C. elegans) FEM1B AF293841 APG5 autophagy 5-like (S. cerevisiae) APG5L BC002809 “down-regulator of transcription 1, TBP- DR1 binding (negative cofactor 2)” AA524525 zinc finger protein 363 ZNF363 NM_006667 progesterone receptor membrane PGRMC1 component 1 K03226 “plasminogen activator, urokinase” PLAU NM_007278 GABA(A) receptor-associated protein GABARAP BC000454 “calmodulin 1 (phosphorylase kinase, CALM1 delta)” NM_006923 stromal cell-derived factor 2 SDF2 BC003133 HLA-B associated transcript 3 BAT3 M27487 “major histocompatibility complex, class II, HLA-DPA1 DP alpha 1” AV702405 emopamil binding protein (sterol isomerase) EBP NM_004639 HLA-B associated transcript 3 BAT3 AF254087 zinc finger protein 278 ZNF278 NM_021204 E-1 enzyme MASA NM_002070 “guanine nucleotide binding protein (G GNAI2 protein), alpha inhibiting activity polypeptide 2” NM_006754 synaptophysin-like protein SYPL NM_005333 holocytochrome c synthase (cytochrome c HCCS heme-lyase) NM_006461 mitotic spindle coiled-coil related protein DEEPEST NM_003096 small nuclear ribonucleoprotein polypeptide G SNRPG AY007098 hypothetical protein FLJ22405 FLJ22405 NM_003252 TIA1 cytotoxic granule-associated RNA TIAL1 binding protein-like 1 BG250310 “zinc finger protein 36, C3H type-like 1” ZFP36L1 NM_031298 hypothetical protein MGC2963 MGC2963 L76416 SMT3 suppressor of mif two 3 homolog 2 SMT3H2 (yeast) NM_014462 Lsm1 protein LSM1 NM_016542 Mst3 and SOK1-related kinase MST4 AL080183 KIAA0592 protein KIAA0592 D80006 disco-interacting protein 2 (Drosophila) DIP2 homolog NM_020232 hepatocellular carcinoma susceptibility HCCA3 protein NM_004873 BCL2-associated athanogene 5 BAG5 AF113514 monocytic leukemia zinc finger protein- MORF related factor BF718636 “H2A histone family, member Z” H2AFZ BF448062 “ubiquitin-conjugating enzyme E2D 3 UBE2D3 (UBC4/5 homolog, yeast)” NM_014045 low density lipoprotein receptor-related LRP10 protein 10 AF135162 cyclin I CCNI M27319 “calmodulin 1 (phosphorylase kinase, CALM1 delta)” S81916 “Phosphoglycerate kinase {alternatively spliced} [human, phosphoglycerate kinase deficient patient with episodes of muscl, mRNA Partial Mutant, 307 nt]” AI589086 Lysosomal-associated multispanning LAPTM5 membrane protein-5 AL031133 “ESTs, Highly similar to SM32_HUMAN Ubiquitin-like protein SMT3B (Sentrin 2) [H. sapiens]” NM_004890 sperm associated antigen 7 SPAG7 NM_003663 CGG triplet repeat binding protein 1 CGGBP1 AK000818 hypothetical protein FLJ20811 FLJ20811 BC001465 HBS1-like (S. cerevisiae) HBS1L NM_021970 mitogen-activated protein kinase kinase 1 MAP2K1IP1 interacting protein 1 M80469 M60333 “major histocompatibility complex, class II, HLA-DRA DR alpha” BG028844 HLA-B associated transcript 3 BAT3 NM_007049 “butyrophilin, subfamily 2, member A1” BTN2A1 AW514210 “ESTs, Highly similar to A60384 MHC class I histocompatibility antigen HLA-F alpha chain Dew3 precursor - human [H. sapiens]” AK024823 SMT3 suppressor of mif two 3 homolog 2 SMT3H2 (yeast)

TABLE 8D Genes discriminating L-asparaginase resistant and sensitive B-lineage ALL to the 0.001 < p < 0.01 level by both T-test and Wilcoxon: Genes up-regulated in L-asparaginase resistant B-lineage ALL NCBI Accession Number Gene Name Gene Symbol L05095 hypothetical protein FLJ22875 FLJ22875 NM_001015 ribosomal protein S11 RPS11 NM_002136 heterogeneous nuclear ribonucleoprotein A1 HNRPA1 BC004334 ribosomal protein S10 RPS10 AI200589 ribosomal protein S16 RPS16 NM_001686 “ATP synthase, H+ transporting, ATP5B mitochondrial F1 complex, beta polypeptide” AF348700 ubiquitin A-52 residue ribosomal protein UBA52 fusion product 1 AA961748 ribosomal protein L13 RPL13 NM_005548 lysyl-tRNA synthetase KARS AI955655 “H3 histone, family 3A” H3F3A BC000524 ribosomal protein S6 RPS6 NM_000979 ribosomal protein L18 RPL18 NM_001997 Finkel-Biskis-Reilly murine sarcoma virus FAU (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 AA630314 ribosomal protein S2 RPS2 NM_001010 ribosomal protein S6 RPS6 AW574664 ribosomal protein L13 RPL13 BC000354 ribosomal protein S28 RPS28 NM_000973 ribosomal protein L8 RPL8 BF247371 hypothetical protein PRO1843 PRO1843 BC001675 ribosomal protein L13a RPL13A NM_001004 “ribosomal protein, large P2” RPLP2 BE968801 ribosomal protein L35a RPL35A NM_001014 ribosomal protein S10 RPS10 BC004886 ribosomal protein S17 RPS17 BF979419 “ESTs, Highly similar to R13A_HUMAN 60S ribosomal protein L13a (23 kDa highly basic protein) [H. sapiens]” AI560573 ribosomal protein L24 RPL24 AA877641 “adaptor-related protein complex 2, alpha 2 AP2A2 subunit” BG152979 ribosomal protein L22 RPL22 BE259729 ribosomal protein S19 RPS19 NM_003640 “inhibitor of kappa light polypeptide gene IKBKAP enhancer in B-cells, kinase complex- associated protein” NM_001021 ribosomal protein S17 RPS17 NM_022551 ribosomal protein S18 RPS18 NM_000990 ribosomal protein L27a RPL27A D17652 ribosomal protein L22 RPL22 NM_001054 “sulfotransferase family, cytosolic, 1A, SULT1A2 phenol-preferring, member 2” BE869922 “H3 histone, family 3A” H3F3A AI805587 ribosomal protein S7 RPS7 NM_004544 “NADH dehydrogenase (ubiquinone) 1 NDUFA10 alpha subcomplex, 10, 42 kDa” AB055804 prefoldin 5 PFDN5 BE963164 “ESTs, Highly similar to S22655 translation elongation factor eEF-1 gamma chain - human [H. sapiens]” NM_007273 repressor of estrogen receptor activity REA NM_001022 ribosomal protein S19 RPS19 NM_000986 ribosomal protein L24 RPL24 NM_000034 “aldolase A, fructose-bisphosphate” ALDOA NM_001013 ribosomal protein S9 RPS9 AF061832 heterogeneous nuclear ribonucleoprotein M HNRPM AI004246 eukaryotic translation elongation factor 2 EEF2 AI970731 ribosomal protein S7 RPS7 AI613273 chromodomain helicase DNA binding CHD4 protein 4 U14990 ribosomal protein S3 RPS3 BF942308 ribosomal protein L13a RPL13A AA888388 ribosomal protein S25 RPS25 BG389744 ribosomal protein L7 RPL7 AL118502 X74070 basic transcription factor 3 BTF3 NM_000991 ribosomal protein L28 RPL28 BE741754 ribosomal protein S6 RPS6 NM_012423 ribosomal protein L13a RPL13A NM_015043 KIAA0676 protein KIAA0676 AF322111 KIAA1049 protein KIAA1049 AK026577 “aldolase A, fructose-bisphosphate” ALDOA NM_000975 ribosomal protein L11 RPL11 NM_003363 ubiquitin specific protease 4 (proto- USP4 oncogene) NM_016400 Huntingtin interacting protein K HYPK NM_002624 prefoldin 5 PFDN5 X89894 “nuclear receptor subfamily 4, group A, NR4A3 member 3” NM_016406 hypothetical protein HSPC155 HSPC155 NM_001961 eukaryotic translation elongation factor 2 EEF2 AA477655 “H3 histone, family 3A” H3F3A BF312331 “H3 histone, family 3A” H3F3A NM_006098 “guanine nucleotide binding protein (G GNB2L1 protein), beta polypeptide 2-like 1” NM_001012 ribosomal protein S8 RPS8 AW304232 “ESTs, Highly similar to RSP4_HUMAN 40S ribosomal protein SA (P40) (34/67 kDa laminin receptor) (Colon carcinoma laminin-binding protein) (NEM/1CHD4) [H. sapiens]” BC005863 “ribosomal protein, large, P0” RPLP0 NM_007104 ribosomal protein L10a RPL10A NM_005594 nascent-polypeptide-associated complex NACA alpha polypeptide NM_030662 mitogen-activated protein kinase kinase 2 MAP2K2 NM_001404 eukaryotic translation elongation factor 1 EEF1G gamma AL530441 “casein kinase 1, gamma 2” CSNK1G2 U78525 “eukaryotic translation initiation factor 3, EIF3S9 subunit 9 eta, 116 kDa” BC003655 “ribosomal protein, large, P0” RPLP0 NM_001834 “clathrin, light polypeptide (Lcb)” CLTB NM_001020 ribosomal protein S16 RPS16 NM_007032 Tara-like protein HRIHFB2122 NM_000968 ribosomal protein L4 RPL4 R83000 basic transcription factor 3 BTF3 NM_002954 ribosomal protein S27a RPS27A BF431488 DIPB protein HSA249128 BC006301 anaphase promoting complex subunit 5 ANAPC5 NM_002096 “general transcription factor IIF, GTF2F1 polypeptide 1, 74 kDa” AK001196 KIAA0676 protein KIAA0676 NM_005886 katanin p80 (WD40-containing) subunit B 1 KATNB1 AV746402 hypothetical protein MGC19556 MGC19556 NM_001018 ribosomal protein S15 RPS15 NM_004597 small nuclear ribonucleoprotein D2 SNRPD2 polypeptide 16.5 kDa AF141870 “interleukin enhancer binding factor 3, ILF3 90 kDa” AC004692 AF119850 NM_001002 “ribosomal protein, large, P0” RPLP0 NM_015654 DKFZP564C103 protein DKFZP564C103 AA838274 ribosomal protein L14 RPL14 BE348997 ribosomal protein S9 RPS9 AB014576 KIAA0676 protein KIAA0676 N71116 “phospholipase A2, group IVB (cytosolic)” PLA2G4B AI953822 “ribosomal protein, large, P0” RPLP0 AB007931 retinoblastoma-associated factor 600 RBAF600 BC005817 ribosomal protein L4 RPL4 AB019691 A kinase (PRKA) anchor protein (yotiao) 9 AKAP9 NM_000972 ribosomal protein L7a RPL7A BC000120 “general transcription factor IIF, GTF2F1 polypeptide 1, 74 kDa” NM_003751 “eukaryotic translation initiation factor 3, EIF3S9 subunit 9 eta, 116 kDa” AL512760 fatty acid desaturase 1 FADS1 AB011173 KIAA0601 protein KIAA0601 NM_017802 hypothetical protein FLJ20397 FLJ20397 NM_003169 suppressor of Ty 5 homolog (S. cerevisiae) SUPT5H AI953886 ribosomal protein L4 RPL4 U58766 tissue specific transplantation antigen P35B TSTA3 AF001549 U63131 CDC37 cell division cycle 37 homolog (S. cerevisiae) CDC37 BG230614 “CD47 antigen (Rh-related antigen, CD47 integrin-associated signal transducer)” NM_001207 basic transcription factor 3 BTF3 NM_024662 hypothetical protein FLJ10774 FLJ10774 Y15521 acetylserotonin O-methyltransferase-like ASMTL AK001684 “ATPase, Ca++ transporting, type 2C, ATP2C1 member 1” AF091085 serologically defined breast cancer antigen SDBCAG84 84 NM_021640 chromosome 12 open reading frame 10 C12orf10 NM_006833 “COP9 subunit 6 (MOV34 homolog, 34 kD)” MOV34-34KD NM_000969 ribosomal protein L5 RPL5 NM_004768 “splicing factor, arginine/serine-rich 11” SFRS11 NM_001770 CD19 antigen CD19 NM_002967 scaffold attachment factor B SAFB NM_003756 “eukaryotic translation initiation factor 3, EIF3S3 subunit 3 gamma, 40 kDa” NM_024733 hypothetical protein FLJ14345 FLJ14345 BC000478 heat shock 70 kDa protein 9B (mortalin-2) HSPA9B L48784 BF976260 nascent-polypeptide-associated complex NACA alpha polypeptide NM_001273 chromodomain helicase DNA binding CHD4 protein 4 BG339228 ribosomal protein L3 RPL3 NM_031213 “hypothetical protein MGC: 5244,” MGC NM_002743 protein kinase C substrate 80K-H PRKCSH NM_000970 ribosomal protein L6 RPL6 AF085358 muscle specific gene M9 AF116273 BCL2-associated athanogene BAG1 BC000580 putative proline 4-hydroxylase PH-4 Z98200 “ESTs, Weakly similar to RL3_HUMAN 60S ribosomal protein L3 (HIV-1 TAR RNA binding protein B) (TARBP-B) [H. sapiens]” AY024365 integrin-linked kinase-associated ILKAP serine/threonine phosphatase 2C AB007457 TP53 target gene 1 TP53TG1 NM_013265 chromosome 11 open reading frame2 C11orf2 AF102988 “phospholipase A2, group VI (cytosolic, PLA2G6 calcium-independent)” BF214492 ribosomal protein L5 RPL5 NM_013417 isoleucine-tRNA synthetase IARS AC005011 BC001689 “solute carrier family 25 SLC25A20 (carnitine/acylcarnitine translocase), member 20” AA191576 “nucleophosmin (nucleolar phosphoprotein NPM1 B23, numatrin)” AK026096 KIAA0676 protein KIAA0676 NM_003812 a disintegrin and metalloproteinase domain ADAM23 23 AF119846 muscle specific gene M9 NM_017724 leucine rich repeat (in FLII) interacting LRRFIP2 protein 2 BE737030 “chaperonin containing TCP1, subunit 6A CCT6A (zeta 1)” AL043112 hypermethylated in cancer 2 HIC2 AW083133 muscle specific gene M9 AW245400 tyrosyl-tRNA synthetase YARS NM_006876 “UDP-GlcNAc: betaGal beta-1,3-N- B3GNT6 acetylglucosaminyltransferase 6” AW582267 ribosomal protein L29 RPL29 NM_000967 ribosomal protein L3 RPL3 NM_018119 hypothetical protein FLJ10509 FLJ10509 NM_018555 zinc finger protein 331; zinc finger protein ZNF361 463 BC006483 ribosomal protein L3 RPL3 T33068 anaphase promoting complex subunit 5 ANAPC5 NM_015414 ribosomal protein L36 RPL36 NM_003827 “N-ethylmaleimide-sensitive factor NAPA attachment protein, alpha” NM_016091 “eukaryotic translation initiation factor 3, EIF3S6IP subunit 6 interacting protein” NM_014649 KIAA0138 gene product KIAA0138 NM_015710 glioma tumor suppressor candidate region GLTSCR2 gene 2 BG403834 “Homo sapiens cDNA FLJ20717 fis, clone HEP18380” L22453 AI653608 leucine-rich PPR-motif containing LRPPRC AI744084 hypothetical protein FLJ20850 FLJ20850 BC006332 “clathrin, light polypeptide (Lcb)” CLTB AF251059 hypothetical protein DKFZp761P1010 DKFZp761P1010 NM_002826 quiescin Q6 QSCN6 AF315951 BC002799 KIAA1115 protein KIAA1115 U90268 cerebral cavernous malformations 1 CCM1 BC000514 ribosomal protein L13a RPL13A NM_015909 neuroblastoma-amplified protein NAG AK024909 “Homo sapiens cDNA: FLJ21256 fis, clone COL01402” U87954 “Human erbB3 binding protein EBP1 mRNA, complete cds” BE670928 “MDN1, midasin homolog (yeast)” MDN1 BG029530 jumonji homolog (mouse) JMJ U25804 “caspase 4, apoptosis-related cysteine CASP4 protease” BF246115 “Homo sapiens, RNA helicase-related protein, clone MGC: 32732 IMAGE: 4041046, mRNA, complete cds” L12387 sorcin SRI AV727381 ubiquinol-cytochrome c reductase core UQCRC2 protein II NM_001055 “sulfotransferase family, cytosolic, 1A, SULT1A1 phenol-preferring, member 1” AW451954 adaptor-associated kinase 1 AAK1 AL558875 splicing factor proline/glutamine rich SFPQ (polypyrimidine tract binding protein associated) BC003086 hypothetical protein FLJ20011 FLJ20011 NM_003753 “eukaryotic translation initiation factor 3, EIF3S7 subunit 7 zeta, 66/67 kDa” NM_024656 hypothetical protein FLJ22329 FLJ22329 L25275 “sulfotransferase family, cytosolic, 1A, SULT1A3 phenol-preferring, member 3” NM_002198 interferon regulatory factor 1 IRF1 NM_015057 KIAA0916 protein KIAA0916 NM_001009 ribosomal protein S5 RPS5 NM_006360 dendritic cell protein GA17 AB029290 microtubule-actin crosslinking factor 1 MACF1 BG256504 KIAA0220 protein KIAA0220 BE250348 ribosomal protein L22 RPL22 NM_004445 EphB6 EPHB6 NM_001959 eukaryotic translation elongation factor 1 EEF1B2 beta 2 NM_000544 “transporter 2, ATP-binding cassette, sub- TAP2 family B (MDR/TAP)” AW071997 ribosomal protein L22 RPL22 BC002977 mel transforming oncogene (derived from MEL cell line NK14)-RAB8 homolog NM_022644 chorionic somatomammotropin hormone 2 CSH2 NM_007170 testis-specific kinase 2 TESK2 NM_013447 “egf-like module containing, mucin-like, EMR2 hormone receptor-like sequence 2” NM_000175 glucose phosphate isomerase GPI AF060511 “Homo sapiens cDNA: FLJ23602 fis, clone LNG15735” BC001081 anaphase promoting complex subunit 5 ANAPC5 BC002827 tropomyosin 4 TPM4 NM_004417 dual specificity phosphatase 1 DUSP1 AA406605 weakly similar to glutathione peroxidase 2 CL683 NM_001910 cathepsin E CTSE BE968833 “spectrin, beta, non-erythrocytic 1” SPTBN1 NM_005051 glutaminyl-tRNA synthetase QARS NM_006360 dendritic cell protein GA17 BC002629 B-cell CLL/lymphoma 7A BCL7A NM_006817 chromosome 12 open reading frame 8 C12orf8 AK024034 “Homo sapiens cDNA FLJ13972 fis, clone Y79AA1001548, highly similar to PHOSPHATIDYLINOSITOL 4-KINASE ALPHA (EC 2.7.1.67)” NM_016527 hydroxyacid oxidase 2 (long chain) HAO2 AA555113 “ribosomal protein, large, P0” RPLP0 BE540552 fatty acid desaturase 1 FADS1 BE042354 lactate dehydrogenase B LDHB AA206161 KIAA0182 protein KIAA0182 N80922 UDP-glucuronic acid/UDP-N- UGTREL7 acetylgalactosamine dual transporter NM_002194 inositol polyphosphate-1-phosphatase INPP1 U80918 “nuclear factor of activated T-cells, NFATC1 cytoplasmic, calcineurin-dependent 1” AF006011 “dishevelled, dsh homolog 1 (Drosophila)” DVL1 NM_002300 lactate dehydrogenase B LDHB NM_018188 hypothetical protein FLJ10709 FLJ10709 NM_003028 “Homo sapiens cDNA FLJ38908 fis, clone NT2NE2005358” AA156721 activated leukocyte cell adhesion molecule ALCAM NM_024569 hypothetical protein FLJ21047 FLJ21047 AA527238 nucleoporin 98 kDa NUP98 AA443762 “guanine nucleotide binding protein (G GNB2L1 protein), beta polypeptide 2-like 1” NM_018170 hypothetical protein FLJ10656 FLJ10656 NM_015216 KIAA0433 protein KIAA0433 AW024383 ribosomal protein S21 RPS21 NM_024615 hypothetical protein FLJ21308 FLJ21308 AA845710 F-box and WD-40 domain protein 3 FBXW3 AK002111 karyopherin alpha 6 (importin alpha 7) KPNA6 NM_024075 leukocyte receptor cluster (LRC) member 5 LENG5 NM_002971 special AT-rich sequence binding protein 1 SATB1 (binds to nuclear matrix/scaffold- associating DNA's) NM_016594 “FK506 binding protein 11, 19 kDa” FKBP11 NM_023925 hypothetical protein FLJ22569 FLJ22569 NM_024537 hypothetical protein FLJ12118 FLJ12118 U64898 nardilysin (N-arginine dibasic convertase) NRD1 M29277 melanoma cell adhesion molecule MCAM NM_002147 homeo box B5 HOXB5 NM_006893 ligatin LGTN NM_006680 “malic enzyme 3, NADP(+)-dependent, ME3 mitochondrial” NM_001778 CD48 antigen (B-cell membrane protein) CD48 NM_013366 anaphase-promoting complex subunit 2 APC2 BF676980 “glutamate-cysteine ligase, catalytic GCLC subunit” M30448 NM_014038 basic leucine zipper and W2 domains 2 BZW2 NM_017967 hypothetical protein FLJ20850 FLJ20850 AF087481 putative DNA/chromatin binding motif PLU-1 NM_024653 hypothetical protein FLJ13902 FLJ13902 NM_014254 transmembrane protein 5 TMEM5 NM_003105 “sortilin-related receptor, L(DLR class) A SORL1 repeats-containing” AI613045 “neurotrophic tyrosine kinase, receptor, type NTRK3 3” NM_005013 nucleobindin 2 NUCB2 AI214061 tropomyosin 4 TPM4 NM_000366 tropomyosin 1 (alpha) TPM1 BG476661 cell division cycle 34 CDC34 NM_015367 MIL1 protein MIL1 NM_004528 microsomal glutathione S-transferase 3 MGST3 NM_014367 “hypothetical protein, estradiol-induced” E2IG5 NM_007274 brain acyl-CoA hydrolase BACH AI971258 seven in absentia homolog 1 (Drosophila) SIAH1 NM_000512 “galactosamine (N-acetyl)-6-sulfate GALNS sulfatase (Morquio syndrome, mucopolysaccharidosis type IVA)” BE792224 distal-less homeo box 2 DLX2 NM_018373 synaptojanin 2 binding protein SYNJ2BP AF181660 myelin protein zero-like 1 MPZL1 NM_004327 breakpoint cluster region BCR D89976 5-aminoimidazole-4-carboxamide ATIC ribonucleotide formyltransferase/IMP cyclohydrolase AK023938 “Homo sapiens cDNA FLJ13876 fis, clone THYRO1001401” AL161999 cytoplasmic FMR1 interacting protein 2 CYFIP2 J02959 leukotriene A4 hydrolase LTA4H AK026142 ocular development-associated gene ODAG AF274935 putative membrane protein LOC54499 AV705803 Homo sapiens mRNA; cDNA DKFZp667K0521 (from clone DKFZp667K0521) NM_000884 IMP (inosine monophosphate) IMPDH2 dehydrogenase 2 NM_024852 hypothetical protein FLJ12765 FLJ12765 NM_016055 mitochondrial ribosomal protein L48 MRPL48 U03891 “apolipoprotein B mRNA editing enzyme, APOBEC3A catalytic polypeptide-like 3A” AL117405 KIAA0673 protein KIAA0673 AB002363 KIAA0365 gene product KIAA0365 NM_003570 cytidine monophosphate-N- CMAH acetylneuraminic acid hydroxylase (CMP- N-acetylneuraminate monooxygenase) NM_020202 Nit protein 2 NIT2 NM_005384 “nuclear factor, interleukin 3 regulated” NFIL3 NM_017664 hypothetical protein FLJ20093 FLJ20093 NM_020993 B-cell CLL/lymphoma 7A BCL7A NM_006870 destrin (actin depolymerizing factor) DSTN NM_017688 hypothetical protein FLJ20150 FLJ20150 NM_007066 “protein kinase (cAMP-dependent, PKIG catalytic) inhibitor gamma” NM_024068 hypothetical protein MGC2731 MGC2731 BF514079 Kruppel-like factor 4 (gut) KLF4 NM_001674 activating transcription factor 3 ATF3 AI817942 zeta-chain (TCR) associated protein kinase ZAP70 70 kDa NM_014229 “solute carrier family 6 (neurotransmitter SLC6A11 transporter, GABA), member 11” NM_017864 hypothetical protein FLJ20530 FLJ20530 BE964361 melanoma cell adhesion molecule MCAM NM_006194 paired box gene 9 PAX9 NM_015380 CGI-51 protein CGI-51 NM_020070 immunoglobulin lambda-like polypeptide 1 IGLL1 NM_018945 phosphodiesterase 7B PDE7B NM_003573 latent transforming growth factor beta LTBP4 binding protein 4 NM_025092 hypothetical protein FLJ22635 FLJ22635 NM_000658 autoimmune regulator (automimmune AIRE polyendocrinopathy candidiasis ectodermal dystrophy) BC003164 leukocyte receptor cluster (LRC) member 4 LENG4 NM_000170 “glycine dehydrogenase (decarboxylating; GLDC glycine decarboxylase, glycine cleavage system protein P)” NM_018467 uncharacterized hematopoietic MDS032 stem/progenitor cells protein MDS032 D86957 KIAA0202 protein KIAA0202 AL121891 likely ortholog of mouse ubiquitin UBCE7IP5 conjugating enzyme 7 interacting protein 5 NM_017709 hypothetical protein FLJ20202 FLJ20202 NM_018419 SRY (sex determining region Y)-box 18 SOX18 AA723370 CGI-105 protein LOC51011 NM_005213 cystatin A (stefin A) CSTA AI675173 prostaglandin E receptor 4 (subtype EP4) PTGER4 AL021786 integral membrane protein 2A ITM2A NM_001451 forkhead box F1 FOXF1 NM_024830 hypothetical protein FLJ12443 FLJ12443 NM_024749 hypothetical protein FLJ12505 FLJ12505 AB002301 KIAA0303 protein KIAA0303 NM_001553 insulin-like growth factor binding protein 7 IGFBP7 L19185 peroxiredoxin 2 PRDX2 NM_004935 cyclin-dependent kinase 5 CDK5 AB002366 KIAA0368 protein KIAA0368 AL080169 DKFZP434C171 protein DKFZP434C171 AA897516 prostaglandin E receptor 4 (subtype EP4) PTGER4 NM_006885 AT-binding transcription factor 1 ATBF1 NM_018700 tripartite motif-containing 36 TRIM36 NM_002923 “regulator of G-protein signalling 2, 24 kDa” RGS2 BG165833 fatty acid desaturase 1 FADS1 AP001745 chromosome 21 open reading frame 25 C21orf25 AL137651 Homo sapiens mRNA; cDNA DKFZp434O0213 (from clone DKFZp434O0213); partial cds BC005810 stem cell growth factor; lymphocyte SCGF secreted C-type lectin NM_001498 “glutamate-cysteine ligase, catalytic GCLC subunit” NM_021114 “serine protease inhibitor, Kazal type, 2 SPINK2 (acrosin-trypsin inhibitor)” NM_002922 regulator of G-protein signalling 1 RGS1 NM_001174 Rho GTPase activating protein 6 ARHGAP6 NM_018100 hypothetical protein FLJ10466 FLJ10466 D86586 stem cell growth factor; lymphocyte SCGF secreted C-type lectin BC003070 GATA binding protein 3 GATA3 NM_018027 hypothetical protein FLJ10210 FLJ10210 AI524125 protocadherin 9 PCDH9 NM_001197 BCL2-interacting killer (apoptosis- BIK inducing) NM_002975 stem cell growth factor; lymphocyte SCGF secreted C-type lectin S59049 regulator of G-protein signalling 1 RGS1 NM_001673 asparagine synthetase ASNS AB020626 KIAA0819 protein KIAA0819 AF127764 “calpain 3, (p94)” CAPN3 AB035266 neurexin 2 NRXN2 NM_024426 Wilms tumor 1 WT1 AW663712 KIAA0754 protein KIAA0754 AV711904 tudor repeat associator with PCTAIRE 2 PCTAIRE2BP AI978623 KIAA0657 protein KIAA0657 AL080170 BIA2 BIA2 NM_001553 insulin-like growth factor binding protein 7 IGFBP7 AI796169 GATA binding protein 3 GATA3 AI796169 GATA binding protein 3 GATA3

TABLE 9A Top genes discriminating daunorubicin resistant and sensitive B- lineage ALL: Genes down-regulated in daunorubicin resistant B-lineage NCBI Accession Probe ID Gene Name Gene Symbol R/S ratio Number 205062_x_at retinoblastoma binding RBBP1 0.73 NM_002892 protein 1 200059_s_at ras homolog gene family, ARHA 0.75 BC001360 member A 205070_at inhibitor of growth ING3 0.76 NM_019071 family, member 3 202521_at CCCTC-binding factor CTCF 0.71 NM_006565 (zinc finger protein) 219119_at LSM8 homolog, U6 LSM8 0.70 NM_016200 small nuclear RNA associated 218438_s_at endothelial-derived gene 1 EG1 0.67 NM_025205 202777_at soc-2 suppressor of clear SHOC2 0.67 NM_007373 homolog (C. elegans) 213264_at mitogen-activated protein MAP3K12 0.40 AW025150 kinase kinase kinase 12 218010_x_at chromosome 20 open C20orf149 0.74 NM_024299 reading frame 149 222251_s_at glucocorticoid GMEB2 0.67 AL133646 modulatory element binding protein 2 213061_s_at hypothetical protein LOC123803 0.58 AA643304 LOC123803 208735_s_at conserved gene amplified OS4 0.71 AF022231 in osteosarcoma

TABLE 9B Top genes discriminating daunorubicin resistant and sensitive B- lineage ALL: Genes up-regulated in daunorubicin resistant B-lineage NCBI Gene R/S Accession Probe ID Gene Name Symbol ratio Number 207452_s_at contactin 5 CNTN5 1.82 NM_014361 210966_x_at likely ortholog of LARP 1.27 BC001460 mouse la related protein 219737_s_at protocadherin 9 PCDH9 2.97 AI524125 203887_s_at thrombomodulin THBD 1.61 NM_000361 201694_s_at early growth EGR1 1.83 NM_001964 response 1 204401_at K intermediate/small KCNN4 1.75 NM_002250 conductance calcium- activated channel 209429_x_at eukaryotic translation EIF2B4 1.49 AF112207 initiation factor 2B, subunit 4 delta 201184_s_at chromodomain CHD4 1.47 NM_001273 helicase DNA binding protein 4 209953_s_at CDC37 cell division CDC37 1.39 U63131 cycle 37 homolog (S. cerevisiae) 220948_s_at ATPase, Na+/K+ ATP1A1 1.41 NM_000701 transporting, alpha 1 polypeptide

TABLE 9C Genes discriminating daunorubicin resistant and sensitive B-lineage ALL to the 0.001 < p < 0.01 level by both T-test and Wilcoxon: Genes up- regulated in daunorubicin resistant B-lineage NCBI Accession Gene Number Gene Name Symbol NM_018042 hypothetical protein FLJ10260 FLJ10260 D55696 legumain LGMN NM_000165 “gap junction protein, alpha 1, 43 kDa (connexin GJA1 43)” NM_002234 “potassium voltage-gated channel, shaker-related KCNA5 subfamily, member 5” NM_003919 “sarcoglycan, epsilon” SGCE AK025206 “Homo sapiens cDNA: FLJ21553 fis, clone COL06329” NM_030953 tigger transposable element derived 6 TIGD6 AF195953 J04132 “CD3Z antigen, zeta polypeptide (TiT3 CD3Z complex)” BG340670 immunoglobulin heavy constant mu IGHM AW025150 mitogen-activated protein kinase kinase kinase 12 MAP3K12 AW168948 stromal antigen 1 STAG1 NM_018455 uncharacterized bone marrow protein BM039 BM039 Z39557 Homo sapiens clone 23705 mRNA sequence NM_006640 MLL septin-like fusion MSF AV694732 cullin 4B CUL4B AB032261 stearoyl-CoA desaturase (delta-9-desaturase) SCD NM_014791 maternal embryonic leucine zipper kinase MELK NM_007246 “kelch-like 2, Mayven (Drosophila)” KLHL2 AK026236 nucleoporin 160 kDa NUP160 AA643304 Homo sapiens mRNA; cDNA DKFZp666E058 (from clone DKFZp666E058) AW272611 thymopoietin TMPO BC000731 synaptogyrin 1 SYNGR1 NM_002835 “protein tyrosine phosphatase, non-receptor type PTPN12 12” AF151853 preimplantation protein 3 PREI3 BG164064 ubiquitin-conjugating enzyme E2 variant 1 UBE2V1 NM_015928 androgen-induced prostate proliferative shutoff AS3 associated protein AI718418 “stress 70 protein chaperone, microsome- STCH associated, 60 kDa” NM_006717 spindlin SPIN NM_007106 ubiquitin-like 3 UBL3 AI571798 Rho GDP dissociation inhibitor (GDI) alpha ARHGDIA BG338532 SMT3 suppressor of mif two 3 homolog 1 (yeast) SMT3H1 AW139179 fem-1 homolog b (C. elegans) FEM1B AI817061 “protein phosphatase 1, regulatory (inhibitor) PPP1R12A subunit 12A” NM_025205 endothelial-derived gene 1 EG1 AW006345 “signal sequence receptor, alpha (translocon- SSR1 associated protein alpha)” BG390306 spinocerebellar ataxia 7 (olivopontocerebellar SCA7 atrophy with retinal degeneration) NM_004583 “RAB5C, member RAS oncogene family” RAB5C NM_001227 “caspase 7, apoptosis-related cysteine protease” CASP7 AL133646 glucocorticoid modulatory element binding GMEB2 protein 2 AB033078 sphingosine-1-phosphate lyase 1 SGPL1 NM_007373 soc-2 suppressor of clear homolog (C. elegans) SHOC2 AK025348 “Homo sapiens cDNA: FLJ21695 fis, clone COL09653” AF032105 spinocerebellar ataxia 7 (olivopontocerebellar SCA7 atrophy with retinal degeneration) NM_016200 U6 snRNA-associated Sm-like protein LSm8 LOC51691 NM_002358 MAD2 mitotic arrest deficient-like 1 (yeast) MAD2L1 NM_006218 “phosphoinositide-3-kinase, catalytic, alpha PIK3CA polypeptide” NM_004830 “cofactor required for Sp1 transcriptional CRSP3 activation, subunit 3, 130 kDa” AI872408 likely ortholog of mouse variant polyadenylation CSTF2T protein CSTF-64 AF022231 conserved gene amplified in osteosarcoma OS4 NM_014744 “TBC1 domain family, member 5” TBC1D5 NM_002892 retinoblastoma binding protein 1 RBBP1 J03263 lysosomal-associated membrane protein 1 LAMP1 NM_006565 CCCTC-binding factor (zinc finger protein) CTCF NM_005663 Wolf-Hirschhorn syndrome candidate 2 WHSC2 BG289800 “SWI/SNF related, matrix associated, actin SMARCE1 dependent regulator of chromatin, subfamily e, member 1” NM_015153 PHD finger protein 3 PHF3 NM_005359 “MAD, mothers against decapentaplegic homolog MADH4 4 (Drosophila)” AU146275 zinc finger protein 161 ZNF161 NM_014628 gene predicted from cDNA with a complete KIAA0110 coding sequence AI671747 likely ortholog of mouse MAPK-interacting and MISS spindle-stabilizing protein NM_004203 membrane-associated tyrosine- and threonine- PKMYT1 specific cdc2-inhibitory kinase NM_015986 cytokine receptor-like factor 3 CRLF3 BC000383 Wilms' tumour 1-associating protein WTAP NM_014045 low density lipoprotein receptor-related protein LRP10 10 BF001666 Homo sapiens clone 23870 mRNA sequence NM_030969 hypothetical protein MGC1223 MGC1223 AL079310 high-mobility group protein 2-like 1 HMG2L1 NM_024299 chromosome 20 open reading frame 149 C20orf149 AI769416 “CCR4-NOT transcription complex, subunit 8” CNOT8 M80776 “adrenergic, beta, receptor kinase 1” ADRBK1 NM_020232 hepatocellular carcinoma susceptibility protein HCCA3 NM_006327 translocase of inner mitochondrial membrane 23 TIMM23 homolog (yeast) NM_018604 WW domain-containing adapter with a coiled- WAC coil region NM_019071 “inhibitor of growth family, member 3” ING3 NM_024612 hypothetical protein FLJ22060 FLJ22060 AI688580 SRB7 suppressor of RNA polymerase B homolog SURB7 (yeast) AL136629 TSPY-like TSPYL NM_014892 KIAA1116 protein KIAA1116 AL136598 protein associated with PRK1 AWP1 BE465032 hypothetical protein FLJ12619 FLJ12619 AI694023 hypothetical protein DKFZp761F0118 DKFZp761F0118 AA045183 glucocorticoid modulatory element binding GMEB2 protein 2 AI199589 chromosome 20 open reading frame 67 C20orf67 NM_004124 “glia maturation factor, beta” GMFB AA643304 Homo sapiens mRNA; cDNA DKFZp666E058 (from clone DKFZp666E058) AA580004 ADP-ribosylation factor 1 ARF1 BC000903 high-mobility group box 2 HMGB2 AU157515 CDC10 cell division cycle 10 homolog (S. cerevisiae) CDC10 BC006462 ubiquitin-like 1 (sentrin) UBL1 Z25435 NM_024738 hypothetical protein FLJ21415 FLJ21415 AL534321 DAZ associated protein 2 DAZAP2 AF305239 homeodomain interacting protein kinase 3 HIPK3 NM_006826 “tyrosine 3-monooxygenase/tryptophan 5- YWHAQ monooxygenase activation protein, theta polypeptide” NM_006323 “SEC24 related gene family, member B (S. cerevisiae)” SEC24B NM_007234 dynactin 3 (p22) DCTN3 BC001360 “ras homolog gene family, member A” ARHA AU146596 KIAA0553 protein KIAA0553 AA004757 zinc finger protein 236 ZNF236 BF430956 PHD finger protein 3 PHF3 BE962615 sorting nexin 3 SNX3 U69546 “CUG triplet repeat, RNA binding protein 2” CUGBP2 AA919115 “RAB14, member RAS oncogene family” RAB14 NM_016014 CGI-67 protein LOC51104 NM_020191 mitochondrial ribosomal protein S22 MRPS22 AF062483 sorting nexin 3 SNX3 N64681 WD repeat endosomal protein KIAA1449 L76416 SMT3 suppressor of mif two 3 homolog 2 (yeast) SMT3H2 NM_014764 DAZ associated protein 2 DAZAP2 AF202092 autophagy Apg3p/Aut1p-like APG3 BC005876 “ATPase, H+ transporting, lysosomal 21 kDa, V0 ATP6V0B subunit c”” NM_003769 “splicing factor, arginine/serine-rich 9” SFRS9 AF135162 cyclin I CCNI AL117620 vitiligo-associated protein VIT-1 VIT1 BC001465 HBS1-like (S. cerevisiae) HBS1L

TABLE 9D Genes discriminating daunorubicin resistant and sensitive B-lineage ALL to the 0.001 < p < 0.01 level by both T-test and Wilcoxon: Genes down- regulated in daunorubicin resistant B-lineage NCBI Accession Gene Number Gene Name Symbol AL050217 Homo sapiens mRNA; cDNA DKFZp586I0523 (from clone DKFZp586I0523) NM_006392 nucleolar protein 5A (56 kDa with KKE/D repeat) NOL5A AW082913 SFRS protein kinase 1 SRPK1 NM_015953 eNOS interacting protein NOSIP AI613273 chromodomain helicase DNA binding protein 4 CHD4 NM_023935 chromosome 20 open reading frame 116 C20orf116 AL110273 “spectrin, alpha, non-erythrocytic 1 (alpha- SPTAN1 fodrin)” AB007931 retinoblastoma-associated factor 600 RBAF600 NM_001754 runt-related transcription factor 1 (acute myeloid RUNX1 leukemia 1; aml1 oncogene) AU144792 “Homo sapiens cDNA FLJ10127 fis, clone HEMBA1002973, moderately similar to CAMP- DEPENDENT 3′,5′-CYCLIC PHOSPHODIESTERASE 4B (EC 3.1.4.17)” BC001460 KIAA0731 protein KIAA0731 AV738039 KIAA0365 gene product KIAA0365 NM_001239 cyclin H CCNH NM_005566 lactate dehydrogenase A LDHA BC001686 “methionine adenosyltransferase II, alpha” MAT2A NM_012237 sirtuin silent mating type information regulation 2 SIRT2 homolog 2 (S. cerevisiae) Y15521 acetylserotonin O-methyltransferase-like ASMTL NM_015367 MIL1 protein MIL1 NM_002162 intercellular adhesion molecule 3 ICAM3 NM_007295 “breast cancer 1, early onset” BRCA1 U63131 CDC37 cell division cycle 37 homolog (S. cerevisiae) CDC37 NM_000701 “ATPase, Na+/K+ transporting, alpha 1 ATP1A1 polypeptide” NM_001273 chromodomain helicase DNA binding protein 4 CHD4 NM_002820 parathyroid hormone-like hormone PTHLH AA191576 “nucleophosmin (nucleolar phosphoprotein B23, NPM1 numatrin)” NM_007272 chymotrypsin C (caldecrin) CTRC NM_014905 glutaminase GLS L32185 “solute carrier family 11 (proton-coupled divalent SLC11A1 metal ion transporters), member 1” NM_000674 adenosine A1 receptor ADORA1 BG484069 “Fanconi anemia, complementation group A” FANCA AI819238 “inhibitor of DNA binding 2, dominant negative ID2 helix-loop-helix protein” AF125393 “RAB27A, member RAS oncogene family” RAB27A AW050627 “centaurin, alpha 1” CENTA1 AF112207 translation initiation factor eIF-2b delta subunit EIF2B AF051782 diaphanous homolog 1 (Drosophila) DIAPH1 AF157324 similar to S. cerevisiae RER1 RER1 AV733950 early growth response 1 EGR1 AB011126 formin-binding protein 17 FBP17 AC004382 hypothetical protein DKFZp434K046 DKFZP434K046 NM_001108 “acylphosphatase 2, muscle type” ACYP2 NM_012323 v-maf musculoaponeurotic fibrosarcoma MAFF oncogene homolog F (avian) NM_006554 metaxin 2 MTX2 NM_016202 LDL induced EC protein LOC51157 BG251266 FOS-like antigen 1 FOSL1 NM_001964 early growth response 1 EGR1 BF061658 “transforming growth factor, beta 2” TGFB2 NM_000247 MHC class I polypeptide-related sequence A MICA NM_001544 “intercellular adhesion molecule 4, Landsteiner- ICAM4 Wiener blood group” NM_019076 “UDP glycosyltransferase 1 family, polypeptide UGT1A A cluster” NM_000361 thrombomodulin THBD NM_003236 “transforming growth factor, alpha” TGFA NM_004418 dual specificity phosphatase 2 DUSP2 NM_002250 “potassium intermediate/small conductance KCNN4 calcium-activated channel, subfamily N, member 4” NM_000641 interleukin 11 IL11 NM_021153 “cadherin 19, type 2” CDH19 NM_004049 BCL2-related protein A1 BCL2A1 NM_014361 contactin 5 CNTN5 NM_025092 hypothetical protein FLJ22635 FLJ22635 BC003070 GATA binding protein 3 GATA3 NM_000399 “early growth response 2 (Krox-20 homolog, EGR2 Drosophila)” NM_002207 “integrin, alpha 9” ITGA9 AI524125 protocadherin 9 PCDH9 AI796169 GATA binding protein 3 GATA3

TABLE 10A Genes discriminating prednisolone resistant and sensitive ALL B- and T-lineage ALL): Genes down-regulated in prednisolone resistant ALL NCBI R/S Accession Probe ID Gene Name Gene Symbol ratio Number 212726_at PHD finger protein 2 PHF2 0.51 AB014562 213061_s_at hypothetical protein LOC123803 0.68 AA643304 LOC123803 212167_s_at SWI/SNF related, matrix SMARCB1 0.82 AK021419 associated, actin dependent regulator 209675_s_at E1B-55 kDa-associated E1B-AP5 0.65 BC004242 protein 5 217729_s_at amino-terminal enhancer AES 0.71 NM_001130.3 of split 208620_at poly(rC) binding protein 1 PCBP1 0.68 U24223 203274_at coagulation factor VIII- F8A 0.61 NM_012151 associated (intronic transcript) 218438_s_at endothelial-derived gene 1 EG1 0.72 NM_025205 210092_at mago-nashi homolog, MAGOH 0.76 AF067173 proliferation-associated (Drosophila) 208739_x_at SMT3 suppressor of mif two SMT3H2 0.72 L76416 3 homolog 2 (yeast) 218381_s_at U2 small nuclear U2AF65 0.81 NM_007279 ribonucleoprotein auxiliary factor (65 kD) 210053_at Homo sapiens mRNA; 0.54 AW138827 cDNA DKFZp434I1626 201821_s_at translocase of inner TIMM17A 0.67 BC004439 mitochondrial membrane 17 homolog A 212180_at v-crk sarcoma virus CT10 CRKL 0.74 AK000311 oncogene homolog (avian)-like 208765_s_at heterogeneous nuclear HNRPR 0.70 NM_005826 ribonucleoprotein R 38710_at ubiquitin-specific protease FLJ20113 0.81 AL096714 otubain 1 212100_s_at KIAA1649 protein KIAA1649 0.85 Z93241 203521_s_at endocrine regulator ZFP318 0.49 NM_014345 206865_at harakiri, BCL2 interacting HRK 0.30 U76376 protein (contains only BH3 domain) 209760_at KIAA0922 protein KIAA0922 0.68 AL136932

TABLE 10B Genes discriminating prednisolone resistant and sensitive ALL (B- and T-lineage ALL): Genes up-regulated in prednisolone resistant ALL NCBI Accession Probe ID Gene Name Gene Symbol R/S ratio Number 206209_s_at carbonic anhydrase IV CA4 1.48 NM_000717 210423_s_at solute carrier family 11 SLC11A1 1.41 L32185 206267_s_at megakaryocyte-associated MATK 2.18 NM_002378 tyrosine kinase 206905_s_at matrilin 1, cartilage matrix MATN1 1.86 NM_002379 protein 210140_at cystatin F (leukocystatin) CST7 2.21 AF031824 207988_s_at actin related protein 2/3 ARPC2 1.25 NM_005731 complex, subunit 2, 34 kDa 201061_s_at stomatin STOM 1.79 M81635 214057_at myeloid cell leukemia MCL1 1.60 H71805 sequence 1 (BCL2- related) 216907_x_at killer cell KIR3DL2 1.32 X93596 immunoglobulin-like receptor 202771_at KIAA0233 gene product KIAA0233 2.17 NM_014745 219380_x_at polymerase (DNA POLH 1.89 NM_006502 directed), eta 203139_at death-associated protein DAPK1 1.71 NM_004938 kinase 1

TABLE 11A Genes discriminating vincristine resistant and sensitive ALL (B- and T-lineage ALL): Genes down-regulated in vincristine resistant ALL NCBI R/S Accession Probe ID Gene Name Gene Symbol ratio Number 212210_at DKFZP586J0619 protein DKFZP586J0619 0.47 AB037861 200593_s_at heterogeneous nuclear HNRPU 0.77 BC003621 ribonucleoprotein U (scaffold attachmen 217733_s_at thymosin, beta 10 TMSB10 0.87 NM_021103 200809_x_at ribosomal protein L12 RPL12 0.84 NM_000976 200088_x_at cDNA (AK026491) 0.81 AK026491 214271_x_at ribosomal protein L12 RPL12 0.83 AA281332 200725_x_at ribosomal protein L10 RPL10 0.85 NM_006013 200061_s_at ribosomal protein S24 RPS24 0.78 BC000523 213084_x_at ribosomal protein L23a RPL23A 0.81 BF125158 208825_x_at ribosomal protein L23a RPL23A 0.81 U43701 208834_x_at ribosomal protein L23a RPL23A 0.78 BC001865 200963_x_at ribosomal protein L31 RPL31 0.82 NM_000993 213377_x_at complement component 1, C1S 0.83 AI799007 s subcomponent 200781_s_at ribosomal protein S15a RPS15A 0.80 NM_001019 200909_s_at ribosomal protein, large P2 RPLP2 0.86 NM_001004 212433_x_at ribosomal protein S2 RPS2 0.79 AA630314 200680_x_at high-mobility group box 1 HMGB1 0.83 NM_002128 201268_at non-metastatic cells 2, NME2 0.71 NM_002512 protein (NM23B) expressed in 204559_s_at LSM7 homolog, U6 small LSM7 0.76 NM_016199 nuclear RNA associated 218608_at putative ATPase HSA9947 0.18 NM_022089 214369_s_at RAS guanyl releasing RASGRP2 0.65 AI688812 protein 2 (calcium and DAG-regulated) 218672_at hypothetical protein MGC3180 0.75 NM_024041 MGC3180 204490_s_at CD44 antigen (homing CD44 0.43 M24915 function and Indian blood group system) 201426_s_at ribosomal protein, large RPLP2 0.58 AI922599 P2

TABLE 11B Genes discriminating vincristine resistant and sensitive ALL (B- and T-lineage ALL): Genes up-regulated in vincristine resistant ALL NCBI R/S Accession Probe ID Gene Name Gene Symbol ratio Number 212335_at glucosamine (N-acetyl)-6- GNS 1.45 AW167793 sulfatase (Sanfilippo disease IIID) 218647_s_at hypothetical protein FLJ23476 1.31 NM_024640 FLJ23476 213225_at protein phosphatase 1B PPM1B 1.37 AJ271832 (formerly 2C), magnesium- dependent 201088_at karyopherin alpha 2 (RAG KPNA2 1.40 NM_002266 cohort 1, importin alpha 1) 202392_s_at phosphatidylserine PISD 1.26 NM_014338 decarboxylase 213604_at Homo sapiens clone 24582 1.29 AW451236 mRNA sequence 212049_at Homo sapiens cDNA 1.19 AK026913 FLJ30463 fis, clone BRACE2009517. 221752_at slingshot 1 SSH1 1.19 AB037719 200757_s_at calumenin CALU 1.22 NM_001219 215127_s_at RNA binding motif, single RBMS1 1.33 AL517946 stranded interacting protein 1 204434_at spermatogenesis associated 2 SPATA2 1.34 NM_006038 55872_at KIAA1196 protein KIAA1196 1.45 AI493119 210791_s_at Rho GTPase-activating RICS 1.59 BC000277 protein 215616_s_at KIAA0876 protein KIAA0876 2.72 AB020683 212492_s_at KIAA0876 protein KIAA0876 1.45 AW237172 210187_at FK506 binding protein 1A, FKBP1A 1.35 BC005147 12 kDa 212345_s_at hypothetical protein DKFZP586F2423 1.47 BE675139 DKFZp586F2423 213301_x_at transcriptional TIF1 2.46 AL538264 intermediary factor 1 204391_x_at transcriptional TIF1 2.56 NM_015905 intermediary factor 1 37986_at erythropoietin receptor EPOR 2.19 M60459 212438_at putative nucleic acid RY1 1.40 BG252325 binding protein RY-1 213939_s_at Homo sapiens cDNA 3.63 AI871641 FLJ12012 fis, clone HEMBB1001668. 213017_at abhydrolase domain ABHD3 1.93 AL534702 containing 3 221011_s_at likely ortholog of mouse LBH 1.45 NM_030915 limb-bud and heart gene 44790_s_at chromosome 13 open C13orf18 2.06 AI129310 reading frame 18 206574_s_at protein tyrosine PTP4A3 2.10 NM_007079 phosphatase type IVA, member 3 209695_at protein tyrosine PTP4A3 1.69 BC003105 phosphatase type IVA, member 3 206033_s_at desmocollin 3 DSC3 1.71 NM_001941 206231_at K intermediate/small KCNN1 1.65 NM_002248 conductance calcium- activated channel 208056_s_at core-binding factor, runt CBFA2T3 1.50 NM_005187 domain, alpha subunit 2; translocated t

TABLE 12A Genes discriminating L-asparaginase resistant and sensitive ALL (B- and T-lineage ALL): Genes down-regulated in L-asparaginase resistant ALL NCBI Accession Probe ID Gene Name Gene Symbol R/S ratio Number 217602_at peptidylprolyl isomerase PPIA 0.66 AI191118 A (cyclophilin A) 208656_s_at cyclin I CCNI 0.85 AF135162 218802_at hypothetical protein FLJ20647 0.65 NM_017918 FLJ20647 203388_at arrestin, beta 2 ARRB2 0.70 NM_004313 202557_at stress 70 protein STCH 0.68 AI718418 chaperone, microsome- associated 216862_s_at mature T-cell MTCP1 0.72 Z24459 proliferation 1 218027_at mitochondrial ribosomal MRPL15 0.69 NM_014175 protein L15 203094_at gene predicted from CMT2 0.78 NM_014628 cDNA with a complete coding sequence 201668_x_at myristoylated alanine- MARCKS 0.53 AW163148 rich protein kinase C substrate 201670_s_at myristoylated alanine- MARCKS 0.27 M68956 rich protein kinase C substrate 201669_s_at myristoylated alanine- MARCKS 0.20 NM_002356 rich protein kinase C substrate 211255_x_at death effector domain DEDD 0.81 AF064605 containing 203521_s_at endocrine regulator ZFP318 0.58 NM_014345 218614_at hypothetical protein FLJ10652 0.72 NM_018169 FLJ10652 212749_s_at zinc finger protein 363 ZNF363 0.77 AL050144 211559_s_at cyclin G2 CCNG2 0.67 L49506 202769_at cyclin G2 CCNG2 0.73 AW134535 200987_x_at proteasome (prosome, PSME3 0.74 AA758755 macropain) activator subunit 3 201376_s_at heterogeneous nuclear HNRPF 0.74 AI591354 ribonucleoprotein F 201140_s_at RAB5C, member RAS RAB5C 0.72 NM_004583 oncogene family 217750_s_at hypothetical protein FLJ13855 0.75 NM_023079 FLJ13855 203311_s_at ADP-ribosylation factor 6 ARF6 0.67 M57763 212643_at chromosome 14 open C14orf32 0.78 AI671747 reading frame 32 218333_at CGI-101 protein F-LAN-1 0.74 NM_016041 218438_s_at endothelial-derived gene 1 EG1 0.79 NM_025205 203274_at coagulation factor VIII- F8A 0.70 NM_012151 associated (intronic transcript) 212544_at thyroid hormone receptor TRIP3 0.82 AI131008 interactor 3 205644_s_at small nuclear SNRPG 0.74 NM_003096 ribonucleoprotein polypeptide G 208739_x_at SMT3 suppressor of mif SMT3H2 0.81 L76416 two 3 homolog 2 (yeast)

TABLE 12B Genes discriminating L-asparaginase resistant and sensitive ALL (B- and T-lineage ALL): Genes up-regulated in L-asparaginase resistant ALL NCBI Accession Probe ID Gene Name Gene Symbol R/S ratio Number 212792_at KIAA0877 protein KIAA0877 1.73 AB020684 204770_at transporter 2, ATP- TAP2 1.32 NM_000544 binding cassette, sub- family B (MDR/TAP) 215544_s_at ortholog of mouse UBCE7IP5 1.40 AL121891 ubiquitin conjugating enzyme 7 interacting pr 215115_x_at neurotrophic tyrosine NTRK3 1.34 AI613045 kinase, receptor, type 3 216344_at nephronophthisis 4 NPHP4 1.47 AL117405 210501_x_at large tumor suppressor, 1.26 AF119846 Drosophila) homolog 1 200034_s_at ribosomal protein L6 RPL6 1.28 NM_000970 217807_s_at glioma tumor suppressor GLTSCR2 1.32 NM_015710 candidate region gene 2 200010_at ribosomal protein L11 RPL11 1.22 NM_000975 217740_x_at ribosomal protein L7a RPL7A 1.23 NM_000972 201217_x_at ribosomal protein L3 RPL3 1.33 NM_000967 208692_at ribosomal protein S3 RPS3 1.21 U14990 220306_at hypothetical protein FLJ20202 1.77 NM_017709 FLJ20202 204897_at prostaglandin E receptor PTGER4 2.54 NM_000958 4 (subtype EP4) 219833_s_at hypothetical protein FLJ10466 2.20 NM_018100 FLJ10466 212886_at DKFZP434C171 protein DKFZP434C171 1.87 AL080169 60528_at phospholipase A2, group PLA2G4B 1.17 N71116 IVB (cytosolic) 214873_at Homo sapiens mRNA; DKFZp434O0213 2.70 AL137651 cDNA 202315_s_at breakpoint cluster region BCR 1.48 NM_004327 212715_s_at KIAA0819 protein KIAA0819 2.56 AB020626 204836_at glycine dehydrogenase GLDC 1.67 NM_000170 206335_at galactosamine (N- GALNS 1.45 NM_000512 acetyl)-6-sulfate sulfatase 216908_x_at RNA polymerase I RRN3 1.21 AF001549 transcription factor RRN3

TABLE 13A Genes discriminating daunorubicin resistant and sensitive ALL (B- and T-lineage ALL): Genes down-regulated in daunorubicin resistant ALL NCBI Gene R/S Accession Probe ID Gene Name Symbol ratio Number 213061_s_at hypothetical protein LOC123803 0.61 AA643304 LOC123803 203112_s_at Wolf-Hirschhorn WHSC2 0.70 NM_005663 syndrome candidate 2 218438_s_at endothelial-derived EG1 0.70 NM_025205 gene 1 202777_at soc-2 suppressor of SHOC2 0.63 NM_007373 clear homolog (C. elegans) 222251_s_at glucocorticoid GMEB2 0.71 AL133646 modulatory element binding protein 2 205070_at inhibitor of growth ING3 0.76 NM_019071 family, member 3 213264_at mitogen-activated MAP3K12 0.39 AW025150 protein kinase kinase kinase 12 218010_x_at chromosome 20 C20orf149 0.76 NM_024299 open reading frame 149

TABLE 13B Genes discriminating daunorubicin resistant and sensitive ALL (B- and T-lineage ALL): Genes up-regulated in daunorubicin resistant ALL NCBI Gene R/S Accession Probe ID Gene Name Symbol ratio Number 203517_at metaxin 2 MTX2 1.60 NM_006554 209429_x_at eukaryotic EIF2B4 1.43 AF112207 translation initiation factor 2B, subunit 4 delta 204401_at K intermediate/small KCNN4 1.70 NM_002250 conductance calcium-activated channel 210423_s_at solute carrier SLC11A1 1.33 L32185 family 11 204794_at dual specificity DUSP2 2.09 NM_004418 phosphatase 2 201184_s_at chromodomain CHD4 1.29 NM_001273 helicase DNA binding protein 4 207194_s_at intercellular ICAM4 1.49 NM_001544 adhesion molecule 4

C. Expression of Cellular Resistance Genes and Treatment Outcome.

For the 173 patients evaluated, the median follow-up was 4.2 years; 132 remain in continuous complete remission and 40 patients have relapsed and 1 patients had a competing event (second malignancy) that was censored at the time of occurrence. A higher combined gene expression score indicative of resistance to the four drugs, was significantly associated with an increased risk of relapse (FIG. 1 a, P=0.001). The combined drug resistance gene expression score was also predictive in a multivariate analysis including known prognostic factors, age and white blood cell count (Hazard ratio=3.39, P=0.007, for patients with a high drug resistance gene expression score versus a low drug resistance gene score.

To assess the robustness of the drug-resistance gene expression profiles in discriminating treatment outcome, the combined gene expression score was tested in a completely independent cohort of 98 patients with acute lymphoblastic leukemia who had been treated with these antileukemic agents, but on a different protocol at St. Jude Children's Research Hospital. The median follow-up of these patients was 7.0 years; 17 had relapsed; 9 had competing events and 72 remained in continuous complete remission. As was the case for patients treated in Europe, a higher combined drug resistance gene expression score was significantly associated with a higher risk of relapse in the independent test set (FIG. 1 b, P=0.003). Moreover, when genetic subtypes, lineage, age and white blood cell count at diagnosis were included in a multivariate analysis, the combined drug resistance gene expression score was independently related to a higher probability of disease relapse in this independent test set (Hazard ratio=11.85, P=0.019 for patients with a high drug resistance gene expression score versus a low drug resistance gene score).

D. Gene Ontology Classification of Discriminating Genes.

Genes discriminating resistance to each antileukemic agent in B-lineage acute lymphoblastic leukemia were grouped in defined functional categories according to the Gene Ontology database. For prednisolone, the percentage of genes involved in metabolism (i.e., carbohydrate metabolism) was higher in the subgroup of 42 discriminating gene probe sets (25 percent) compared to the entire genome (11 percent, P=0.039). For vincristine, genes involved in nucleic acid metabolism (39 percent versus 23 percent, P=0.021) and for L-asparaginase, protein metabolism genes (53 percent versus 20 percent, P<0.001) were over-represented in the group of genes that were associated with drug resistance, compared to the entire genome. Supplemental FIG. 12 depicts the functional groups associated with drug resistance when both immunophenotypes were included in the analyses.

E. Expression of Genes Previously Linked with Drug Resistance or Prognosis in Acute Leukemia.

The great majority of differentially expressed genes that we identified (120 of 123) have not been previously linked to drug resistance for the four agents investigated. Only three genes that were significant in our analyses, (i.e., RPL6, ARHA and SLC2A14) have been previously associated with resistance to doxorubicin (RPL6,25 ARHA,26) or vincristine (SLC2A1427). When the expression of 46 additional genes that encode proteins previously associated with drug resistance or prognosis was compared in sensitive and resistant acute lymphoblastic leukemia, 12 of those genes were differentially expressed for at least one drug at the P<0.05 level, but none reached the level of significance required for inclusion in the models described above. For example, the gene encoding asparagine synthetase (ASNS) was significantly over-expressed in acute lymphoblastic leukemia that was resistant to L-asparaginase, consistent with previously reported differences in the NCI panel of 60 human cancer cell lines (Scherf et al. (2000) Nat. Genet. 24:236-44; and Weinstein et al. (1997) Science 275:343-49). However, ASNS (P=0.0002, Wilcoxon rank sum test; P=0.0005, t-test) was not among the 54 most discriminating probe sets for L-asparaginase sensitivity, as defined by P<0.0001.

III. Conclusions

The present invention identifies genes that are differentially expressed in acute lymphoblastic leukemia cells that exhibit de novo resistance to widely used antileukemic drugs, and demonstrates that the expression pattern of these genes is related to treatment outcome. The expression of 42, 59, 54 and 22 gene probe sets (representing 123 unique known genes and 30 cDNA clones) in primary B-lineage leukemia cells discriminated cellular resistance to prednisolone, vincristine, L-asparaginase or daunorubicin, respectively. Notably, 120 of the 123 genes discriminating sensitive and resistant acute lymphoblastic leukemia have not been previously associated with cellular resistance to these antileukemic agents to the inventors' knowledge. Twelve genes that have been previously associated with drug resistance or prognosis in acute lymphoblastic leukemia were differentially expressed in acute lymphoblastic leukemia cells resistant to one or more of these drugs (P<0.05), but only three (RPL6, ARHA, SLC2A14) were significant at the level required for inclusion in our models.

No universal “cross-resistance gene” was identified, as no gene was common among genes that discriminated resistance to all four drugs. Discriminating genes belong to numerous functional groups, according to the Gene Ontology (GO) database, and specific functional categories were significantly over-represented for some antileukemic agents. These findings document that resistance to mechanistically distinct antileukemic agents is associated with aberrant expression of different functional groups of genes, in support of combination chemotherapy as the paradigm for cancer treatment. Moreover, these findings point to previously unrecognized targets for developing new agents to augment the efficacy of current chemotherapy acute lymphoblastic leukemia.

Over-expression of the glucose transporter SLC2A14 and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes indicates that prednisolone resistant cells have a higher glycolytic rate than prednisolone sensitive cells. This is consistent with the overrepresentation of carbohydrate metabolism-associated genes among those discriminating prednisolone resistance, compared to the human genome. In addition, prednisolone resistance was associated with down-regulation of several transcription-associated genes (PRPF18, SMARCB1 and CTCF). SMARCB1 is a component of the SWI/SNF chromatin remodeling complex, which has been shown to alter nucleosome conformation in an ATP-dependent manner, leading to increased accessibility of nucleosomal DNA to transcription factors (Muchardt and Yaniv (1999) Semin. Cel.l Dev. Biol. 10:189-95. The glucocorticoid receptor is able to recruit the SWI-SNF complex to target promoters, thereby facilitating glucocorticoid-dependent gene activation (Wallberg et al. (2000) Mol. Cell. Biol. 20:2004-13). The current findings indicate that hampering glucocorticoid-dependent gene activation is associated with prednisolone resistance in acute lymphoblastic leukemia.

Vincristine resistance was associated with altered expression of cytoskeleton or extracellular matrix-associated proteins (e.g., TMSB10 and DSC3). Vincristine is cytotoxic by inhibiting tubulin polymerization and disrupting overall cytoskeletal integrity. Over-expression of TMSB10 induces actin depolymerization, resulting in loss of cytoskeletal integrity and apoptosis (Lee et al. (2001) Oncogene 20:6700-6; and Yu et al. (1993) J. Biol. Chem. 268:502-9). It follows that a high basal level of actin depolymerization sensitizes cells to the effects of a tubulin-depolymerizing agent like vincristine. Indeed, vincristine has been found to work synergistically with the actin depolymerizing agent cytochalasin (Kolber and Hill (1992) Cancer Chemother. Pharmacol. 30:286-90). Thus, these findings indicate that modulation of proteins other than tubulin, such as TMSB10, may offer a strategy to sensitize leukemia cells to vinca alkaloids.

L-asparaginase resistance was associated with over-expression of a large group of ribosomal genes (e.g., RPS3, RPL7A and RPL4) and translation-associated genes (e.g., EEFG1, EEF1B2 and EIF3S7). Expression of some ribosomal proteins has been previously linked to doxorubicin resistance in cell lines (Bertram et al. (1998) Eur. J Cancer 34 (5):731-36; and Lopez et al. (2002) Cancer Lett. 180:195-202), but their contribution to L-asparaginase resistance has not been previously recognized to the best of the inventors knowledge. It should be noted that these prior studies determined the expression of only one or two ribosomal protein members, whereas simultaneous over-expression of a large cluster of ribosomal proteins has not been previously linked to cellular drug resistance. L-asparaginase catalyzes the degradation of asparagine, leading to rapid depletion of the circulating pool of asparagine, and consequent diminution of protein synthesis, at least in part by selective suppression of translation of ribosomal proteins (Iiboshi et al. (1999) Biochem. Biophys. Res. Commun. 260:534-39). The current findings suggest that over-expression of ribosomal- and translation-associated genes in acute lymphoblastic leukemia cells confers L-asparaginase resistance. Although it is not intended that the present invention be limited by any particular mechanism, such resistance may be due to overriding the L-asparaginase-induced block of protein synthesis, by over-expressing proteins involved in the translational machinery. Interestingly, under-expression of a different cluster of ribosomal proteins (e.g., RPS11, RPL12 and RPLP2) was associated with vincristine resistance. Taken together, these findings suggest that different ribosomal proteins may contribute to L-asparaginase and vincristine resistance, revealing a potential new mechanism of resistance and suggesting strategies for modulating sensitivity to these antileukemic agents.

We found that down-regulation of the ARHA (RhoA) gene was associated with daunorubicin resistance. Rho proteins, members of the Ras superfamily of GTPases, are important in signal transduction pathways governing cell proliferation and cell death (Van Aelst et al. (1997) Genes Dev. 11:2295-2322). Treatment of leukemic cell lines with daunorubicin induces ceramide generation (Jaffrezou et al. (1996) EMBO J 15:2417-24) and activation of the CD95/CD95-ligand system (Fulda et al. (2000) Blood 95:301-8; and Belaud-Rotureau et al. (2000) Leukemia 14:1266-75. Activation of the latter has been reported to be completely blocked in doxorubicin-resistant leukemic cells. Friesen et al. (1997) Leukemia 11: 1833-41. Over-expression of Rac1, another Rho family member, induces ceramide production and synthesis of CD95-ligand. Embade et al. (2000) Mol. Biol. Cell. 11:4347-58. The present data are the first to link decreased expression of RhoA with daunorubicin resistance, suggesting that RhoA down-regulation impedes daunorubicin-induced proapoptotic signal transduction pathways. A gene that was over-expressed in daunorubicin resistant acute lymphoblastic leukemia was chromodomain helicase DNA-binding protein 4 (CHD4), a central component of the nucleosome remodeling and histone deacetylation (NRD) complex, which leads to transcriptional repression. Tong (1998) Nature 395:917-21. Indeed, the histone deacetylase inhibitor AN-9 has been shown to sensitize non-leukemic cell lines to the cytotoxicity of daunorubicin and doxorubicin (Niitsu et al. (2000) Mol. Pharmacol. 58:27-36), suggesting that targeting CHD4 and/or inhibiting histone deacetylase may be a new strategy to circumvent daunorubicin resistance in pediatric acute lymphoblastic leukemia.

It is noteworthy that the gene expression signatures identified based on the in vitro sensitivity or resistance of primary leukemia cells to the individual antileukemic agents, were related to overall treatment response. Moreover, the robustness of these gene expression signatures was validated by their ability to discriminate outcome in a completely independent population of patients who were treated with these same drugs, but in a separate country on a different protocol. In a multivariate analysis with other known prognostic variables (i.e., age, white blood cell count, genetic subtype and lineage), the combined gene expression score remained significantly related to the risk of disease relapse (Table 14). The four significant variables with P<0.05 were, presence of the BCR/ABL gene fusion (hazard ratio=14.2), combined drug resistance gene expression score (hazard ratio=11.9), age>10 years (hazard ratio=7.6) and white blood cell count>50×109 per L (hazard ratio=10.2). This indicates that the expression of genes identified as conferring drug resistance, is an independent prognostic feature influencing treatment outcome in childhood acute lymphoblastic leukemia.

TABLE 14(a) Multivariate proportional-hazard analysis of the risk of disease relapse Number of Hazard Ratio Variable patients (95% C.I.) P-value Age 1-10 126 1.0* >10 47 1.83 (0.96, 3.50) 0.068 WBC (10⁹/L)  <10 38 1.0* 10-49 68 0.98 (0.37, 2.63) 0.97 50-99 28 1.36 (0.42, 4.38) 0.61 ≧100 39 4.06 (1.68, 9.77) 0.002 Combined drug resistance gene expression score‡ Low (<4.70) 60 1.0* Intermediate (4.70-5.58) 56 3.02 (1.19, 7.70) 0.020 High (>5.58) 57 3.39 (1.41, 8.17) 0.007

TABLE 14(b) Multivariate proportional-hazard analysis of the risk of disease relapse Number of Hazard Ratio (95% P- Variable patients C.I.) value Age 1-10 62  1.0*  <1 7  6.48 (0.60, 69.79) 0.12 >10 29  7.61 (1.23, 46.95) 0.029 Genetic Subtype B-lineage other 24  1.0* BCR-ABL 8 14.17 (2.59, 77.55) 0.002 E2A-PBX1 12  0.63 (0.07, 6.29) 0.69 MLL-AF4 14  1.23 (0.22, 6.76) 0.81 TEL-AML1 16  1.40 (0.09, 21.36) 0.81 Hyperdiploidy 15  0.92 (0.10, 8.02) 0.94 T-cell 9  4.03 (0.60, 26.89) 0.15 WBC (10⁹/L)  <10 25  1.0* 10-49 27  1.93 (0.24, 15.15) 0.53 50-99 20 12.02 (1.30, 0.028 110.79) ≧100 26  8.35 (0.84, 83.11) 0.070 Combined drug resistance gene expression score‡ Low (<4.70) 29  1.0* Intermediate (4.70-5.58) 48  4.00 (0.58, 27.73) 0.16 High (>5.58) 21 11.85 (1.51, 93.12) 0.019

The identification of gene expression patterns that confer resistance to individual drugs, reveals proteins and pathways that can be targets for the development of new agents to augment the efficacy of current therapy. Because genes that confer sensitivity or resistance differ for each antileukemic agent, these findings point to strategies whereby one could modulate only the components of therapy to which an individual patient is resistant.

All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the invention. 

1. A method of diagnosing drug resistant leukemia in a subject affected by leukemia, the method comprising: a) providing a subject expression profile of a sample from a subject affected by leukemia; b) providing a reference expression profile associated with resistance to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, wherein the subject expression profile and the reference expression profile comprise one or more values representing the expression level of a gene having differential expression in subjects affected by leukemia who are resistant to the antileukemic agent; and c) determining whether the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent; wherein the subject is diagnosed with drug resistant leukemia if the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent.
 2. The method of claim 1, wherein the subject expression profile and the reference expression profile comprise values representing the expression levels of at least 20 genes selected from: (a) the genes shown in Tables 6A, 6B, 6C, 6D, 10A, and 11B; (b) the genes shown in Tables 7A, 7B, 7C, 7D, 11A, and 11B; (c) the genes shown in Tables 8A, 8B, 8C, 8D, 12A, and 12B; and (d) the genes shown in Tables 9A, 9B, 9C, 9D, 13A, and 13B.
 3. The method of claim 2 wherein the antileukemic agent is prednisolone and the subject expression profile and the reference expression profile associated with resistance to the antileukemic agent comprise values representing the expression levels of at least 20 genes selected from the genes shown in Tables 6A, 6B, 6C, 6D, 10A, and 10B.
 4. The method of claim 2 wherein the antileukemic agent is vincristine and the subject expression profile and the reference expression profile associated with resistance to the drug antileukemic agent comprise values representing the expression levels of at least 20 genes selected from the genes shown in Tables 7A, 7B, 7C, 7D, 11A, and 11B.
 5. The method of claim 2 wherein the antileukemic agent is L-asparaginase and the subject expression profile and the reference expression profile associated with resistance to the antileukemic agent comprise values representing the expression levels of at least 20 genes selected from the genes shown in Tables 8A, 8B, 8C, 8D, 12A, and 12B.
 6. The method of claim 2 wherein the antileukemic agent is daunorubicin and the subject expression profile and the reference expression profile associated with resistance to the antileukemic agent comprise values representing the expression levels of at least 20 genes selected from the genes shown in Tables 9A, 9B, 9C, 9D, 13A and 13B.
 7. The method of claim 1, wherein said sample from said subject affected by leukemia comprises leukemic blasts.
 8. The method of claim 1, wherein said sample from said subject affected by leukemia comprises at least 60% leukemic blasts.
 9. The method of claim 8, wherein said sample from said subject affected by leukemia comprises at least 75% leukemic blasts.
 10. The method of claim 1 wherein said sample comprises leukemic blasts derived from peripheral blood.
 11. The method of claim 1 wherein said sample comprises blast cells derived from bone marrow.
 12. A method of selecting a therapy for a subject affected by leukemia, said method comprising the steps of: a) providing a subject expression profile of a sample from said subject affected by leukemia; b) providing a reference expression profile associated with resistance to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, wherein the subject expression profile and the reference expression profile comprise one or more values representing the expression level of a gene having differential expression in subjects affected by leukemia who are resistant to the antileukemic agent; and c) determining whether the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent; wherein the therapy selected for the subject does not comprise the antileukemic agent if the subject expression profile shares sufficient similarity to the reference expression profile associated with resistance to the antileukemic agent.
 13. The method of claim 12, wherein the subject expression profile and the reference expression profile comprise values representing the expression levels of at least 20 genes selected from: (a) the genes shown in Tables 6A, 6B, 6C, 6D, 10A, and 11B; (b) the genes shown in Tables 7A, 7B, 7C, 7D, 11A, and 11B; (c) the genes shown in Tables 8A, 8B, 8C, 8D, 12A, and 12B; and (d) the genes shown in Tables 9A, 9B, 9C, 9D, 13A, and 13B.
 14. A method of selecting a therapy for a subject affected by leukemia, said method comprising the steps of: a) providing a subject expression profile of a sample from said subject affected by leukemia; b) providing a reference expression profile associated with resistance to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, wherein the subject expression profile and the reference expression profile comprise one or more values representing the expression level of a gene having differential expression in subjects affected by leukemia who are resistant to the antileukemic agent; and c) determining whether the subject expression profile is distinguishable from the reference expression profile associated with resistance to the antileukemic agent; wherein the antileukemic agent is selected as a therapy for the subject if the subject expression profile is distinguishable from the reference expression profile associated with resistance to the antileukemic agent.
 15. The method of claim 14, wherein the subject expression profile and the reference expression profile comprise values representing the expression levels of at least 20 genes selected from: (a) the genes shown in Tables 6A, 6B, 6C, 6D, 10A, and 11B; (b) the genes shown in Tables 7A, 7B, 7C, 7D, 11A, and 11B; (c) the genes shown in Tables 8A, 8B, 8C, 8D, 12A, and 12B; and (d) the genes shown in Tables 9A, 9B, 9C, 9D, 13A, and 13B.
 16. A method for screening a library of compounds to identify a compound to improve treatment of drug resistant leukemia, said method comprising the steps of: a) providing a reference expression profile associated with resistance to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, wherein the reference expression profile comprises one or more values representing the expression level of a gene selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B; and b) providing a cell that is resistant to an antileukemic agent; c) contacting the cell with one or more compounds from the library of compounds; d) creating a test expression profile by determining a value representing the expression level in the cell of one or more of the genes whose expression level is represented in the reference expression profile of step a); (c) determining whether the test expression profile is distinguishable from the reference expression profile; wherein the compound is identified as a compound useful for improving treatment of drug resistant leukemia if the test expression profile is distinguishable from the reference expression profile.
 17. The method of claim 16 wherein the cell that is resistant to antileukemic agents is derived from peripheral blood.
 18. The method of claim 16 wherein the cell that is resistant to antileukemic agents is a blast cell derived from bone marrow.
 19. The method of claim 16 wherein the antileukemic agent is prednisolone and the subject expression profile and the reference expression profile associated with resistance to the antileukemic agent comprise values representing the expression levels of at least 20 genes selected from the genes shown in Tables 6A, 6B, 6C, 6D, 10A, and 10B.
 20. The method of claim 16 wherein the antileukemic agent is vincristine and the subject expression profile and the reference expression profile associated with resistance to the drug antileukemic agent comprise values representing the expression levels of at least 20 genes selected from the genes shown in Tables 7A, 7B, 7C, 7D, 11A, and 11B.
 21. The method of claim 16 wherein the antileukemic agent is L-asparaginase and the subject expression profile and the reference expression profile associated with resistance to the antileukemic agent comprise values representing the expression levels of at least 20 genes selected from the genes shown in Tables 8A, 8B, 8C, 8D, 12A, and 12B.
 22. The method of claim 16 wherein the antileukemic agent is daunorubicin and the subject expression profile and the reference expression profile associated with resistance to the antileukemic agent comprise values representing the expression levels of at least 20 genes selected from the genes shown in Tables 9A, 9B, 9C, 9D, 13A, and 13B.
 23. A method for screening a library of compounds to identify a compound to improve treatment of drug resistant leukemia, said method comprising the steps of: a) providing a reference expression profile associated with sensitivity to at least one antileukemic agent selected from prednisolone, vincristine, L-asparaginase, and daunorubicin, wherein the reference expression profile comprises one or more values representing the expression level of a gene selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B; and b) providing a cell that is resistant to an antileukemic agent; c) contacting the cell with one or more compounds from the library of compounds; d) creating a test expression profile by determining a value representing the expression level in the cell of one or more of the genes whose expression level is represented in the reference expression profile of step a); (c) determining whether the test expression profile shares significant similarity with the reference expression profile; wherein the compound is identified as a compound useful for improving treatment of drug resistant leukemia if the test expression profile shares statistically significant similarity with the reference expression profile.
 24. A method for identifying a compound useful for improving treatment of drug resistant leukemia, the method comprising screening a library of compounds to identify a compound that enhances the expression or activity of at least one gene selected from the genes shown in Tables 6A, 6C, 7A, 7C, 8A, 8C, 9A, 9C, 10A, 11A, 12A, and 13A.
 25. An improved method for treating drug resistant leukemia comprising the steps of a) identifying a compound that enhances the expression or activity of at least one gene selected from the genes shown in Tables 6A, 6C, 7A, 7C, 8A, 8C, 9A, 9C, 10A, 11A, 12A, and 13A according to the method of embodiment 24; b) administering to a subject affected by drug resistant leukemia a therapy comprising an antileukemic agent and a compound identified according to step a).
 26. The method of claim 25 wherein the antileukemic agent is prednisolone and the agent that enhances the expression or activity of at least one gene selected from the genes shown in Tables 6A, 6C, and 10A.
 27. The method of claim 25 wherein the antileukemic agent is vincristine and the agent that enhances the expression or activity of at least one gene selected from the genes shown in Tables 7A, 7C, and 11A.
 28. The method of claim 25 wherein the antileukemic agent is L-asparaginase and the agent that enhances the expression or activity of at least one gene selected from the genes shown in Tables 8A, 8C, and 12A.
 29. The method of claim 25 wherein the antileukemic agent is daunorubicin and the agent that enhances the expression or activity of at least one gene selected from the genes shown in Tables 9A, 9C, and 13A.
 30. A method for identifying a compound useful for improving treatment of drug resistant leukemia, the method comprising screening a library of compounds to identify a compound that that inhibits the expression or activity of at least one gene selected from the genes shown in Tables 6B, 6D, 7B, 7D, 8B, 8D, 9B, 9D, 10B, 11B, 12B, and 13B.
 31. An improved method for treating drug resistant leukemia comprising the steps of a) identifying a compound that that inhibits the expression or activity of at least one gene selected from the genes shown in Tables 6B, 6D, 7B, 7D, 8B, 8D, 9B, 9D, 10B, 11B, 12B, and 13B according to the method of embodiment 30; b) administering to a subject affected by drug resistant leukemia a therapy comprising an antileukemic agent and a compound identified according to step a).
 32. The method of claim 31 wherein the antileukemic agent is prednisolone and the agent that inhibits the expression or activity of at least one gene selected from the genes shown in Tables 6B, 6D, and 10B.
 33. The method of claim 31 wherein the antileukemic agent is vincristine and the agent that inhibits the expression or activity of at least one gene selected from the genes shown in Tables 7B, 7D, and 11B.
 34. The method of claim 31 wherein the antileukemic agent is L-asparaginase and the agent that inhibits the expression or activity of at least one gene selected from the genes shown in Tables 8B, 8D, and 12B.
 35. The method of claim 31 wherein the antileukemic agent is daunorubicin and the agent that inhibits the expression or activity of at least one gene selected from the genes shown in Tables 9B, 9D, and 13B.
 36. An array for use in a method of diagnosing drug resistant leukemia comprising a substrate having a plurality of addresses, wherein each address has disposed thereon a capture probe that can specifically bind a nucleic acid molecule selected from the group consisting of genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B, and wherein the array has fewer than 500 addresses.
 37. The array of claim 36, wherein the substrate has greater than 20 addresses.
 38. The array of claim 37, wherein the substrate has greater than 40 addresses.
 39. The array of claim 38, wherein the substrate has greater than 90 addresses.
 40. The array of claim 37 wherein the substrate has fewer than 160 addresses.
 41. A kit for diagnosing drug-resistant leukemia comprising: a) an array according to claim 37; and b) a computer-readable medium having a plurality of digitally-encoded expression profiles wherein each profile of the plurality has a plurality of values, each value representing the expression of a nucleic acid molecule detected by the array.
 42. A computer-readable medium comprising a plurality of digitally-encoded expression profiles wherein each profile of the plurality has at least 20 values, each value representing the expression of a gene selected from the genes shown in Tables 6A, 6B, 6C, 6D, 7A, 7B, 7C, 7D, 8A, 8B, 8C, 8D, 9A, 9B, 9C, 9D, 10A, 10B, 11A, 11B, 12A, 12B, 13A, and 13B. 